1
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Czajka JJ, Han Y, Kim J, Mondo SJ, Hofstad BA, Robles A, Haridas S, Riley R, LaButti K, Pangilinan J, Andreopoulos W, Lipzen A, Yan J, Wang M, Ng V, Grigoriev IV, Spatafora JW, Magnuson JK, Baker SE, Pomraning KR. Genome-scale model development and genomic sequencing of the oleaginous clade Lipomyces. Front Bioeng Biotechnol 2024; 12:1356551. [PMID: 38638323 PMCID: PMC11024372 DOI: 10.3389/fbioe.2024.1356551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 03/12/2024] [Indexed: 04/20/2024] Open
Abstract
The Lipomyces clade contains oleaginous yeast species with advantageous metabolic features for biochemical and biofuel production. Limited knowledge about the metabolic networks of the species and limited tools for genetic engineering have led to a relatively small amount of research on the microbes. Here, a genome-scale metabolic model (GSM) of Lipomyces starkeyi NRRL Y-11557 was built using orthologous protein mappings to model yeast species. Phenotypic growth assays were used to validate the GSM (66% accuracy) and indicated that NRRL Y-11557 utilized diverse carbohydrates but had more limited catabolism of organic acids. The final GSM contained 2,193 reactions, 1,909 metabolites, and 996 genes and was thus named iLst996. The model contained 96 of the annotated carbohydrate-active enzymes. iLst996 predicted a flux distribution in line with oleaginous yeast measurements and was utilized to predict theoretical lipid yields. Twenty-five other yeasts in the Lipomyces clade were then genome sequenced and annotated. Sixteen of the Lipomyces species had orthologs for more than 97% of the iLst996 genes, demonstrating the usefulness of iLst996 as a broad GSM for Lipomyces metabolism. Pathways that diverged from iLst996 mainly revolved around alternate carbon metabolism, with ortholog groups excluding NRRL Y-11557 annotated to be involved in transport, glycerolipid, and starch metabolism, among others. Overall, this study provides a useful modeling tool and data for analyzing and understanding Lipomyces species metabolism and will assist further engineering efforts in Lipomyces.
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Affiliation(s)
- Jeffrey J. Czajka
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
- US Department of Energy Agile BioFoundry, Emeryville, CA, United States
| | - Yichao Han
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
- US Department of Energy Agile BioFoundry, Emeryville, CA, United States
| | - Joonhoon Kim
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
- US Department of Energy Agile BioFoundry, Emeryville, CA, United States
- US Department of Energy Joint BioEnergy Institute, Emeryville, CA, United States
| | - Stephen J. Mondo
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, United States
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Beth A. Hofstad
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
- US Department of Energy Agile BioFoundry, Emeryville, CA, United States
| | - AnaLaura Robles
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
- US Department of Energy Agile BioFoundry, Emeryville, CA, United States
| | - Sajeet Haridas
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Robert Riley
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Kurt LaButti
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Jasmyn Pangilinan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - William Andreopoulos
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Juying Yan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Mei Wang
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Vivian Ng
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Igor V. Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Joseph W. Spatafora
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Jon K. Magnuson
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
- US Department of Energy Agile BioFoundry, Emeryville, CA, United States
- US Department of Energy Joint BioEnergy Institute, Emeryville, CA, United States
| | - Scott E. Baker
- US Department of Energy Agile BioFoundry, Emeryville, CA, United States
- US Department of Energy Joint BioEnergy Institute, Emeryville, CA, United States
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Kyle R. Pomraning
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
- US Department of Energy Agile BioFoundry, Emeryville, CA, United States
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2
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Zhang Y, Nada B, Baker SE, Evans JE, Tian C, Benz JP, Tamayo E. Unveiling a classical mutant in the context of the GH3 β-glucosidase family in Neurospora crassa. AMB Express 2024; 14:4. [PMID: 38180602 PMCID: PMC10770018 DOI: 10.1186/s13568-023-01658-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 12/23/2023] [Indexed: 01/06/2024] Open
Abstract
Classical fungal mutant strains obtained by mutagenesis have helped to elucidate fundamental metabolic pathways in the past. In the filamentous fungus Neurospora crassa, the gluc-1 strain was isolated long ago and characterized by its low level of β-glucosidase activity, which is essential for the degradation of cellulose, the most abundant biopolymer on Earth and the main polymeric component of the plant cell wall. Based on genomic resequencing, we hypothesized that the causative mutation resides in the β-glucosidase gene gh3-3 (bgl6, NCU08755). In this work, growth patterns, enzymatic activities and sugar utilization rates were analyzed in several mutant and overexpression strains related to gluc-1 and gh3-3. In addition, different mutants affected in the degradation and transport of cellobiose were analyzed. While overexpression of gh3-3 led to the recovery of β-glucosidase activity in the gluc-1 mutant, as well as normal utilization of cellobiose, the full gene deletion strain Δgh3-3 was found to behave differently than gluc-1 with lower secreted β-glucosidase activity, indicating a dominant role of the amino acid substitution in the point mutated gh3-3 gene of gluc-1. Our results furthermore confirm that GH3-3 is the major extracellular β-glucosidase in N. crassa and demonstrate that the two cellodextrin transporters CDT-1 and CDT-2 are essential for growth on cellobiose when the three main N. crassa β-glucosidases are absent. Overall, these findings provide valuable insight into the mechanisms of cellulose utilization in filamentous fungi, being an essential step in the efficient production of biorefinable sugars from agricultural and forestry plant biomass.
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Affiliation(s)
- Yuxin Zhang
- Fungal Biotechnology in Wood Science, Holzforschung München, TUM School of Life Sciences, Technical University of Munich, 85354, Freising, Germany
| | - Basant Nada
- Fungal Biotechnology in Wood Science, Holzforschung München, TUM School of Life Sciences, Technical University of Munich, 85354, Freising, Germany
| | - Scott E Baker
- DOE Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Microbial Molecular Phenotyping Group, Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - James E Evans
- Microbial Molecular Phenotyping Group, Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Chaoguang Tian
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - J Philipp Benz
- Fungal Biotechnology in Wood Science, Holzforschung München, TUM School of Life Sciences, Technical University of Munich, 85354, Freising, Germany
| | - Elisabeth Tamayo
- Fungal Biotechnology in Wood Science, Holzforschung München, TUM School of Life Sciences, Technical University of Munich, 85354, Freising, Germany.
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3
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Visagie CM, Magistà D, Ferrara M, Balocchi F, Duong TA, Eichmeier A, Gramaje D, Aylward J, Baker SE, Barnes I, Calhoun S, De Angelis M, Frisvad JC, Hakalova E, Hayes RD, Houbraken J, Grigoriev IV, LaButti K, Leal C, Lipzen A, Ng V, Pangilinan J, Pecenka J, Perrone G, Piso A, Savage E, Spetik M, Wingfield MJ, Zhang Y, Wingfield BD. IMA genome-F18 : The re-identification of Penicillium genomes available in NCBI and draft genomes for Penicillium species from dry cured meat, Penicillium biforme, P. brevicompactum, P. solitum, and P. cvjetkovicii, Pewenomyces kutranfy, Pew. lalenivora, Pew. tapulicola, Pew. kalosus, Teratosphaeria carnegiei, and Trichoderma atroviride SC1. IMA Fungus 2023; 14:21. [PMID: 37803441 PMCID: PMC10559472 DOI: 10.1186/s43008-023-00121-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2023] [Indexed: 10/08/2023] Open
Affiliation(s)
- Cobus M. Visagie
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Donato Magistà
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Via G. Amendola 122/O, 70126 Bari, Italy
| | - Massimo Ferrara
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Via G. Amendola 122/O, 70126 Bari, Italy
| | - Felipe Balocchi
- Department of Plant and Soil Sciences, FABI, University of Pretoria, Pretoria, South Africa
| | - Tuan A. Duong
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Ales Eichmeier
- Instituto de Ciencias de la Vid y del Vino (ICVV), Consejo Superior de Investigaciones Científicas - Universidad de la Rioja - Gobierno de La Rioja, Ctra. LO-20 Salida 13, Finca La Grajera, 26071 Logroño, Spain
| | - David Gramaje
- Instituto de Ciencias de la Vid y del Vino (ICVV), Consejo Superior de Investigaciones Científicas - Universidad de la Rioja - Gobierno de La Rioja, Ctra. LO-20 Salida 13, Finca La Grajera, 26071 Logroño, Spain
| | - Janneke Aylward
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
- Department of Conservation Ecology and Entomology, Stellenbosch University, Matieland, Private Bag X1, Stellenbosch, 7602 South Africa
| | - Scott E. Baker
- Functional and Systems Biology Group, Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354 USA
- DOE Joint Bioenergy Institute, Emeryville, CA 94608 USA
| | - Irene Barnes
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Sara Calhoun
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720 USA
| | - Maria De Angelis
- Department of Soil, Plant and Food Sciences, University of Bari “Aldo Moro”, Via G. Amendola 165/a, 70126 Bari, Italy
| | - Jens C. Frisvad
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 221, 2800 Kgs Lyngby, Denmark
| | - Eliska Hakalova
- Mendeleum - Institute of Genetics, Mendel University in Brno, Valticka 334, 691 44 Lednice, Czech Republic
| | - Richard D. Hayes
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720 USA
| | - Jos Houbraken
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Igor V. Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720 USA
- Department of Plant and Microbial Biology, University of California Berkeley, 110 Koshland Hall, Berkeley, CA 94720 USA
| | - Kurt LaButti
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720 USA
| | - Catarina Leal
- Instituto de Ciencias de la Vid y del Vino (ICVV), Consejo Superior de Investigaciones Científicas - Universidad de la Rioja - Gobierno de La Rioja, Ctra. LO-20 Salida 13, Finca La Grajera, 26071 Logroño, Spain
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720 USA
| | - Vivian Ng
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720 USA
| | - Jasmyn Pangilinan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720 USA
| | - Jakub Pecenka
- Mendeleum - Institute of Genetics, Mendel University in Brno, Valticka 334, 691 44 Lednice, Czech Republic
| | - Giancarlo Perrone
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Via G. Amendola 122/O, 70126 Bari, Italy
| | - Anja Piso
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Emily Savage
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720 USA
| | - Milan Spetik
- Mendeleum - Institute of Genetics, Mendel University in Brno, Valticka 334, 691 44 Lednice, Czech Republic
| | - Michael J. Wingfield
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Yu Zhang
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720 USA
| | - Brenda D. Wingfield
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
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4
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Czajka JJ, Banerjee D, Eng T, Menasalvas J, Yan C, Munoz NM, Poirier BC, Kim YM, Baker SE, Tang YJ, Mukhopadhyay A. Tuning a high performing multiplexed-CRISPRi Pseudomonas putida strain to further enhance indigoidine production. Metab Eng Commun 2022; 15:e00206. [PMID: 36158112 PMCID: PMC9494242 DOI: 10.1016/j.mec.2022.e00206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 09/01/2022] [Accepted: 09/06/2022] [Indexed: 11/30/2022] Open
Abstract
In this study, a 14-gene edited Pseudomonas putida KT2440 strain for heterologous indigoidine production was examined using three distinct omic datasets. Transcriptomic data indicated that CRISPR/dCpf1-interference (CRISPRi) mediated multiplex repression caused global gene expression changes, implying potential undesirable changes in metabolic flux. 13C-metabolic flux analysis (13C-MFA) revealed that the core P. putida flux network after CRISPRi repression was conserved, with moderate reduction of TCA cycle and pyruvate shunt activity along with glyoxylate shunt activation during glucose catabolism. Metabolomic results identified a change in intracellular TCA metabolites and extracellular metabolite secretion profiles (sugars and succinate overflow) in the engineered strains. These omic analyses guided further strain engineering, with a random mutagenesis screen first identifying an optimal ribosome binding site (RBS) for Cpf1 that enabled stronger product-substrate pairing (1.6-fold increase). Then, deletion strains were constructed with excision of the PHA operon (ΔphaAZC-IID) resulting in a 2.2-fold increase in indigoidine titer over the optimized Cpf1-RBS construct at the end of the growth phase (∼6 h). The maximum indigoidine titer (at 72 h) in the ΔphaAZC-IID strain had a 1.5-fold and 1.8-fold increase compared to the optimized Cpf1-RBS construct and the original strain, respectively. Overall, this study demonstrated that integration of omic data types is essential for understanding responses to complex metabolic engineering designs and directly quantified the effect of such modifications on central metabolism.
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Affiliation(s)
- Jeffrey J Czajka
- Department of Energy, Environmental and Chemical Engineering, Washington University, St. Louis, MO, 63130, USA
| | - Deepanwita Banerjee
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Thomas Eng
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Javier Menasalvas
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Chunsheng Yan
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Nathalie Munoz Munoz
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.,Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Brenton C Poirier
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.,Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Young-Mo Kim
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.,Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Scott E Baker
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Yinjie J Tang
- Department of Energy, Environmental and Chemical Engineering, Washington University, St. Louis, MO, 63130, USA
| | - Aindrila Mukhopadhyay
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
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5
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Wilson J, Bilbao A, Wang J, Liao YC, Velickovic D, Wojcik R, Passamonti M, Zhao R, Gargano AFG, Gerbasi VR, Pas̆a-Tolić L, Baker SE, Zhou M. Online Hydrophilic Interaction Chromatography (HILIC) Enhanced Top-Down Mass Spectrometry Characterization of the SARS-CoV-2 Spike Receptor-Binding Domain. Anal Chem 2022; 94:5909-5917. [PMID: 35380435 PMCID: PMC9003935 DOI: 10.1021/acs.analchem.2c00139] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/25/2022] [Indexed: 12/13/2022]
Abstract
SARS-CoV-2 cellular infection is mediated by the heavily glycosylated spike protein. Recombinant versions of the spike protein and the receptor-binding domain (RBD) are necessary for seropositivity assays and can potentially serve as vaccines against viral infection. RBD plays key roles in the spike protein's structure and function, and thus, comprehensive characterization of recombinant RBD is critically important for biopharmaceutical applications. Liquid chromatography coupled to mass spectrometry has been widely used to characterize post-translational modifications in proteins, including glycosylation. Most studies of RBDs were performed at the proteolytic peptide (bottom-up proteomics) or released glycan level because of the technical challenges in resolving highly heterogeneous glycans at the intact protein level. Herein, we evaluated several online separation techniques: (1) C2 reverse-phase liquid chromatography (RPLC), (2) capillary zone electrophoresis (CZE), and (3) acrylamide-based monolithic hydrophilic interaction chromatography (HILIC) to separate intact recombinant RBDs with varying combinations of glycosylations (glycoforms) for top-down mass spectrometry (MS). Within the conditions we explored, the HILIC method was superior to RPLC and CZE at separating RBD glycoforms, which differ significantly in neutral glycan groups. In addition, our top-down analysis readily captured unexpected modifications (e.g., cysteinylation and N-terminal sequence variation) and low abundance, heavily glycosylated proteoforms that may be missed by using glycopeptide data alone. The HILIC top-down MS platform holds great potential in resolving heterogeneous glycoproteins for facile comparison of biosimilars in quality control applications.
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Affiliation(s)
- Jesse
W. Wilson
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, 3335 Innovation Boulevard, Richland, Washington 99354, United States
| | - Aivett Bilbao
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, 3335 Innovation Boulevard, Richland, Washington 99354, United States
| | - Juan Wang
- Biological
Sciences Division, Pacific Northwest National
Laboratories, 902 Battelle
Boulevard, Richland, Washington 99354, United States
| | - Yen-Chen Liao
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, 3335 Innovation Boulevard, Richland, Washington 99354, United States
| | - Dusan Velickovic
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, 3335 Innovation Boulevard, Richland, Washington 99354, United States
| | - Roza Wojcik
- National
Security Directorate, Pacific Northwest
National Laboratories, 902 Battelle Boulevard, Richland, Washington 99354, United States
| | - Marta Passamonti
- Centre
for Analytical Sciences Amsterdam, Amsterdam 1098 XH, The
Netherlands
- Van’t
Hoff Institute for Molecular Sciences, University
of Amsterdam, Amsterdam 1098 XH, The Netherlands
| | - Rui Zhao
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, 3335 Innovation Boulevard, Richland, Washington 99354, United States
| | - Andrea F. G. Gargano
- Centre
for Analytical Sciences Amsterdam, Amsterdam 1098 XH, The
Netherlands
- Van’t
Hoff Institute for Molecular Sciences, University
of Amsterdam, Amsterdam 1098 XH, The Netherlands
| | - Vincent R. Gerbasi
- Biological
Sciences Division, Pacific Northwest National
Laboratories, 902 Battelle
Boulevard, Richland, Washington 99354, United States
| | - Ljiljana Pas̆a-Tolić
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, 3335 Innovation Boulevard, Richland, Washington 99354, United States
| | - Scott E. Baker
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, 3335 Innovation Boulevard, Richland, Washington 99354, United States
| | - Mowei Zhou
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, 3335 Innovation Boulevard, Richland, Washington 99354, United States
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6
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Baker SE, Ayers M, Beausoleil NJ, Belmain SR, Berdoy M, Buckle AP, Cagienard C, Cowan D, Fearn-Daglish J, Goddard P, Golledge HDR, Mullineaux E, Sharp T, Simmons A, Schmolz E. An assessment of animal welfare impacts in wild Norway rat (Rattus norvegicus) management. Anim Welf 2022. [DOI: 10.7120/09627286.31.1.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Norway rats (Rattus norvegicus) are considered one of the most significant vertebrate pests globally, because of their impacts on human and animal health. There are legal and moral obligations to minimise the impacts of wildlife management on animal welfare, yet there are few
data on the relative welfare impacts of rat trapping and baiting methods used in the UK with which to inform management decisions. Two stakeholder workshops were facilitated to assess the relative welfare impacts of six lethal rat management methods using a welfare assessment model. Fifteen
stakeholders including experts in wildlife management, rodent management, rodent biology, animal welfare science, and veterinary science and medicine, participated. The greatest welfare impacts were associated with three baiting methods, anticoagulants, cholecalciferol and non-toxic cellulose
baits (severe to extreme impact for days), and with capture on a glue trap (extreme for hours) with concussive killing (mild to moderate for seconds to minutes); these methods should be considered last resorts from a welfare perspective. Lower impacts were associated with cage trapping (moderate
to severe for hours) with concussive killing (moderate for minutes). The impact of snap trapping was highly variable (no impact to extreme for seconds to minutes). Snap traps should be regulated and tested to identify those that cause rapid unconsciousness; such traps might represent the most
welfare-friendly option assessed for killing rats. Our results can be used to integrate consideration of rat welfare alongside other factors, including cost, efficacy, safety, non-target animal welfare and public acceptability when selecting management methods. We also highlight ways of reducing
welfare impacts and areas where more data are needed.
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Affiliation(s)
- SE Baker
- University of Oxford, Department of Zoology, Oxford, Oxfordshire, UK
| | - M Ayers
- Precision Pest Management Solutions Ltd, Iveson Drive, Leeds LS16 6BG, UK
| | - NJ Beausoleil
- Massey University, Animal Welfare Science and Bioethics Centre, School of Veterinary Science, Palmerston North, 4410, New Zealand
| | - SR Belmain
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent ME4 4TB, UK
| | - M Berdoy
- University of Oxford, Biomedical Services, Oxford, Oxfordshire, UK
| | - AP Buckle
- School of Biological Sciences, The University of Reading, Reading RG6 6AS, UK
| | - C Cagienard
- Pest Solutions, 10 Seaward Place, Glasgow G41 1HH, UK
| | - D Cowan
- Newcastle University, School of Natural and Environmental Sciences, Newcastle, UK
| | | | | | - HDR Golledge
- Universities Federation for Animal Welfare, The Old School, Brewhouse Hill, Wheathampstead AL4 8AN, UK
| | | | - T Sharp
- Vertebrate Pest Research Unit, NSW Department of Primary Industries, Tocal Agricultural Centre, Paterson, NSW, Australia
| | | | - E Schmolz
- German Environment Agency, Section IV 1.4, Berlin, Germany
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7
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McCluskey K, Baker SE. Identifying the gluc- 1 and gluc- 2 mutations in Neurospora crassa by genome resequencing. J Genet 2022; 101:50. [PMID: 36330790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Genome resequencing is an efficient strategy for associating mutant phenotypes with physical genomic loci (Baker 2009). A pilot study of this approach demonstrated that the Neurospora crassa genetic map was critical in narrowing the possible candidate mutations in a strain to a small number in a limited, defined region of the genome (McCluskey et al. 2011). In this study, we utilize a resequencing strategy to identify the mutations underlying the gluc-1 and gluc-2 genes in N. crassa.
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8
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Kim YM, Petzold CJ, Kerkhoven EJ, Baker SE. Editorial: Multi-Omics Technologies for Optimizing Synthetic Biomanufacturing. Front Bioeng Biotechnol 2021; 9:818010. [PMID: 34976996 PMCID: PMC8715011 DOI: 10.3389/fbioe.2021.818010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 11/29/2021] [Indexed: 12/02/2022] Open
Affiliation(s)
- Young-Mo Kim
- Integrative Omics Group, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States
- *Correspondence: Young-Mo Kim,
| | - Christopher J. Petzold
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Eduard J. Kerkhoven
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Scott E. Baker
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States
- Functional and Systems Biology Group, Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
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9
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Ferrara M, Gallo A, Cervini C, Gambacorta L, Solfrizzo M, Baker SE, Perrone G. Evidence of the Involvement of a Cyclase Gene in the Biosynthesis of Ochratoxin A in Aspergillus carbonarius. Toxins (Basel) 2021; 13:toxins13120892. [PMID: 34941729 PMCID: PMC8705981 DOI: 10.3390/toxins13120892] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/03/2021] [Accepted: 12/04/2021] [Indexed: 12/03/2022] Open
Abstract
Ochratoxin A (OTA) is a well-known mycotoxin with wide distribution in food and feed. Fungal genome sequencing has great utility for identifying secondary metabolites gene clusters for known and novel compounds. A comparative analysis of the OTA-biosynthetic cluster in A. steynii, A. westerdijkiae, A. niger, A. carbonarius, and P. nordicum has revealed a high synteny in OTA cluster organization in five structural genes (otaA, otaB, ota, otaR1, and otaD). Moreover, a recent detailed comparative genome analysis of Aspergilli OTA producers led to the identification of a cyclase gene, otaY, located in the OTA cluster between the otaA and otaB genes, encoding for a predicted protein with high similarity to SnoaLs domain. These proteins have been shown to catalyze ring closure steps in the biosynthesis of polyketide antibiotics produced in Streptomyces. In the present study, we demonstrated an upregulation of the cyclase gene in A. carbonarius under OTA permissive conditions, consistent with the expression trends of the other OTA cluster genes and their role in OTA biosynthesis by complete gene deletion. Our results pointed out the involvement of a cyclase gene in OTA biosynthetic pathway for the first time. They represent a step forward in the understanding of the molecular basis of OTA biosynthesis in A. carbonarius.
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Affiliation(s)
- Massimo Ferrara
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), 70126 Bari, Italy; (L.G.); (M.S.); (G.P.)
- Correspondence:
| | - Antonia Gallo
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), 73100 Lecce, Italy;
| | - Carla Cervini
- Applied Mycology Group, Environment and AgriFood Theme, Cranfield University, Cranfield MK43 0AL, UK;
| | - Lucia Gambacorta
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), 70126 Bari, Italy; (L.G.); (M.S.); (G.P.)
| | - Michele Solfrizzo
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), 70126 Bari, Italy; (L.G.); (M.S.); (G.P.)
| | - Scott E. Baker
- Functional and Systems Biology Group, Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA;
- DOE Joint Bioenergy Institute, Emeryville, CA 94608, USA
| | - Giancarlo Perrone
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), 70126 Bari, Italy; (L.G.); (M.S.); (G.P.)
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10
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Tamano K, Takayama H, Yasokawa S, Sano M, Baker SE. Major involvement of two laccase genes in conidial pigment biosynthesis in Aspergillus oryzae. Appl Microbiol Biotechnol 2021; 106:287-300. [PMID: 34889980 DOI: 10.1007/s00253-021-11669-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 10/24/2021] [Accepted: 10/28/2021] [Indexed: 11/29/2022]
Abstract
Wild-type strains of Aspergillus oryzae develop yellow, yellow-green, green, or brown conidia. Previous reports suggested that the conidiation initiates with the biosynthesis of a yellow pigment YWA1 from acetyl-CoA by a polyketide synthase encoded by wA (AO090102000545). This is followed by the conversion to other pigment by a laccase encoded by yA (AO090011000755). Based on orthologous pathways in other Aspergilli, it is reasonable to hypothesize that in addition to yA, AO090102000546 encoding laccase and AO090005000332 encoding Ayg1-like hydrolase play a role in A. oryzae conidial pigment biosynthesis. However, the involvement of these two genes in conidial pigmentation remains unclear. In this study, we tested this hypothesis by assessing the conidial colors of both disruption and overexpression mutants to verify whether AO090102000546 and AO090005000332 were associated with the conidial pigmentation. Observation of single, double, and triple disruptants of these three genes suggested that conidial pigments were synthesized by two laccase genes, AO090011000755 and AO090102000546, whereas Ayg1-like hydrolase gene AO090005000332 was proven to have no obvious association with the synthesis. This was corroborated by observing the phenotype of each overexpression mutant. Interestingly, AO090005000332 overexpression mutant produced smoky yellow-green conidia, different from the wild-type strain. Thus, the AO090005000332-encoded protein is likely to maintain the enzymatic activity. However, the expression level was observed to be one-third of that of AO090102000546 and one-seventh of that of AO090011000755. Consequently, apparent lack of obvious contribution of AO090005000332 to conidial pigmentation could be attributed to its low expression level. Expression analysis indicated similar profiles in several wild-type strains. KEY POINTS: • Conidial pigment biosynthesis after YWA1 mainly involves two laccases in A. oryzae. • Ayg1-like hydrolase in A. oryzae is not obviously involved in conidial pigmentation. • Conidial color is deemed dependent on expression level of two laccases and hydrolase.
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Affiliation(s)
- Koichi Tamano
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo, Hokkaido, 062-8517, Japan. .,AIST-Waseda University Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), AIST, 5-20, Building 63, Nishi-Waseda Campus, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan.
| | - Haruka Takayama
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo, Hokkaido, 062-8517, Japan
| | - Saeko Yasokawa
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo, Hokkaido, 062-8517, Japan
| | - Motoaki Sano
- Genome Biotechnology Laboratory, Kanazawa Institute of Technology, 3-1 Yatsukaho, Hakusan, Ishikawa, 924-0838, Japan
| | - Scott E Baker
- Pacific Northwest National Laboratory, PO Box 99, Richland, WA, 99352, USA
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11
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McNaughton AD, Bredeweg EL, Manzer J, Zucker J, Munoz Munoz N, Burnet MC, Nakayasu ES, Pomraning KR, Merkley ED, Dai Z, Chrisler WB, Baker SE, St. John PC, Kumar N. Bayesian Inference for Integrating Yarrowia lipolytica Multiomics Datasets with Metabolic Modeling. ACS Synth Biol 2021; 10:2968-2981. [PMID: 34636549 DOI: 10.1021/acssynbio.1c00267] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Optimizing the metabolism of microbial cell factories for yields and titers is a critical step for economically viable production of bioproducts and biofuels. In this process, tuning the expression of individual enzymes to obtain the desired pathway flux is a challenging step, in which data from separate multiomics techniques must be integrated with existing biological knowledge to determine where changes should be made. Following a design-build-test-learn strategy, building on recent advances in Bayesian metabolic control analysis, we identify key enzymes in the oleaginous yeast Yarrowia lipolytica that correlate with the production of itaconate by integrating a metabolic model with multiomics measurements. To this extent, we quantify the uncertainty for a variety of key parameters, known as flux control coefficients (FCCs), needed to improve the bioproduction of target metabolites and statistically obtain key correlations between the measured enzymes and boundary flux. Based on the top five significant FCCs and five correlated enzymes, our results show phosphoglycerate mutase, acetyl-CoA synthetase (ACSm), carbonic anhydrase (HCO3E), pyrophosphatase (PPAm), and homoserine dehydrogenase (HSDxi) enzymes in rate-limiting reactions that can lead to increased itaconic acid production.
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Affiliation(s)
- Andrew D. McNaughton
- Earth and Biological Science Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Erin L. Bredeweg
- Earth and Biological Science Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - James Manzer
- Earth and Biological Science Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Jeremy Zucker
- Earth and Biological Science Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Nathalie Munoz Munoz
- Earth and Biological Science Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Meagan C. Burnet
- Earth and Biological Science Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Ernesto S. Nakayasu
- Earth and Biological Science Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Kyle R. Pomraning
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Eric D. Merkley
- National Security Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Ziyu Dai
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - William B. Chrisler
- Earth and Biological Science Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Scott E. Baker
- Earth and Biological Science Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Peter C. St. John
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado 80401, United States
| | - Neeraj Kumar
- Earth and Biological Science Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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12
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Pomraning KR, Dai Z, Munoz N, Kim YM, Gao Y, Deng S, Kim J, Hofstad BA, Swita MS, Lemmon T, Collett JR, Panisko EA, Webb-Robertson BJM, Zucker JD, Nicora CD, De Paoli H, Baker SE, Burnum-Johnson KE, Hillson NJ, Magnuson JK. Integration of Proteomics and Metabolomics Into the Design, Build, Test, Learn Cycle to Improve 3-Hydroxypropionic Acid Production in Aspergillus pseudoterreus. Front Bioeng Biotechnol 2021; 9:603832. [PMID: 33898398 PMCID: PMC8058442 DOI: 10.3389/fbioe.2021.603832] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 03/16/2021] [Indexed: 11/13/2022] Open
Abstract
Biological engineering of microorganisms to produce value-added chemicals is a promising route to sustainable manufacturing. However, overproduction of metabolic intermediates at high titer, rate, and yield from inexpensive substrates is challenging in non-model systems where limited information is available regarding metabolic flux and its control in production conditions. Integrated multi-omic analyses of engineered strains offers an in-depth look at metabolites and proteins directly involved in growth and production of target and non-target bioproducts. Here we applied multi-omic analyses to overproduction of the polymer precursor 3-hydroxypropionic acid (3HP) in the filamentous fungus Aspergillus pseudoterreus. A synthetic pathway consisting of aspartate decarboxylase, beta-alanine pyruvate transaminase, and 3HP dehydrogenase was designed and built for A. pseudoterreus. Strains with single- and multi-copy integration events were isolated and multi-omics analysis consisting of intracellular and extracellular metabolomics and targeted and global proteomics was used to interrogate the strains in shake-flask and bioreactor conditions. Production of a variety of co-products (organic acids and glycerol) and oxidative degradation of 3HP were identified as metabolic pathways competing with 3HP production. Intracellular accumulation of nitrogen as 2,4-diaminobutanoate was identified as an off-target nitrogen sink that may also limit flux through the engineered 3HP pathway. Elimination of the high-expression oxidative 3HP degradation pathway by deletion of a putative malonate semialdehyde dehydrogenase improved the yield of 3HP by 3.4 × after 10 days in shake-flask culture. This is the first report of 3HP production in a filamentous fungus amenable to industrial scale biomanufacturing of organic acids at high titer and low pH.
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Affiliation(s)
- Kyle R Pomraning
- Pacific Northwest National Laboratory, Richland, WA, United States
| | - Ziyu Dai
- Pacific Northwest National Laboratory, Richland, WA, United States
| | - Nathalie Munoz
- Pacific Northwest National Laboratory, Richland, WA, United States
| | - Young-Mo Kim
- Pacific Northwest National Laboratory, Richland, WA, United States
| | - Yuqian Gao
- Pacific Northwest National Laboratory, Richland, WA, United States
| | - Shuang Deng
- Pacific Northwest National Laboratory, Richland, WA, United States
| | - Joonhoon Kim
- Pacific Northwest National Laboratory, Richland, WA, United States.,Joint BioEnergy Institute, Emeryville, CA, United States
| | - Beth A Hofstad
- Pacific Northwest National Laboratory, Richland, WA, United States
| | - Marie S Swita
- Pacific Northwest National Laboratory, Richland, WA, United States
| | - Teresa Lemmon
- Pacific Northwest National Laboratory, Richland, WA, United States
| | - James R Collett
- Pacific Northwest National Laboratory, Richland, WA, United States
| | - Ellen A Panisko
- Pacific Northwest National Laboratory, Richland, WA, United States
| | | | - Jeremy D Zucker
- Pacific Northwest National Laboratory, Richland, WA, United States
| | - Carrie D Nicora
- Pacific Northwest National Laboratory, Richland, WA, United States
| | | | - Scott E Baker
- Pacific Northwest National Laboratory, Richland, WA, United States
| | | | - Nathan J Hillson
- Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Jon K Magnuson
- Pacific Northwest National Laboratory, Richland, WA, United States.,Joint BioEnergy Institute, Emeryville, CA, United States
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13
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Chroumpi T, Peng M, Markillie LM, Mitchell HD, Nicora CD, Hutchinson CM, Paurus V, Tolic N, Clendinen CS, Orr G, Baker SE, Mäkelä MR, de Vries RP. Re-routing of Sugar Catabolism Provides a Better Insight Into Fungal Flexibility in Using Plant Biomass-Derived Monomers as Substrates. Front Bioeng Biotechnol 2021; 9:644216. [PMID: 33763411 PMCID: PMC7982397 DOI: 10.3389/fbioe.2021.644216] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 02/16/2021] [Indexed: 11/13/2022] Open
Abstract
The filamentous ascomycete Aspergillus niger has received increasing interest as a cell factory, being able to efficiently degrade plant cell wall polysaccharides as well as having an extensive metabolism to convert the released monosaccharides into value added compounds. The pentoses D-xylose and L-arabinose are the most abundant monosaccharides in plant biomass after the hexose D-glucose, being major constituents of xylan, pectin and xyloglucan. In this study, the influence of selected pentose catabolic pathway (PCP) deletion strains on growth on plant biomass and re-routing of sugar catabolism was addressed to gain a better understanding of the flexibility of this fungus in using plant biomass-derived monomers. The transcriptome, metabolome and proteome response of three PCP mutant strains, ΔlarAΔxyrAΔxyrB, ΔladAΔxdhAΔsdhA and ΔxkiA, grown on wheat bran (WB) and sugar beet pulp (SBP), was evaluated. Our results showed that despite the absolute impact of these PCP mutations on pure pentose sugars, they are not as critical for growth of A. niger on more complex biomass substrates, such as WB and SBP. However, significant phenotypic variation was observed between the two biomass substrates, but also between the different PCP mutants. This shows that the high sugar heterogeneity of these substrates in combination with the high complexity and adaptability of the fungal sugar metabolism allow for activation of alternative strategies to support growth.
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Affiliation(s)
- Tania Chroumpi
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, Netherlands
| | - Mao Peng
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, Netherlands
| | - Lye Meng Markillie
- Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Hugh D Mitchell
- Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Carrie D Nicora
- Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Chelsea M Hutchinson
- Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Vanessa Paurus
- Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Nikola Tolic
- Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Chaevien S Clendinen
- Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Galya Orr
- Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Scott E Baker
- Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Miia R Mäkelä
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, Netherlands.,Department of Microbiology, University of Helsinki, Helsinki, Finland
| | - Ronald P de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, Netherlands
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14
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Kim J, Coradetti ST, Kim YM, Gao Y, Yaegashi J, Zucker JD, Munoz N, Zink EM, Burnum-Johnson KE, Baker SE, Simmons BA, Skerker JM, Gladden JM, Magnuson JK. Multi-Omics Driven Metabolic Network Reconstruction and Analysis of Lignocellulosic Carbon Utilization in Rhodosporidium toruloides. Front Bioeng Biotechnol 2021; 8:612832. [PMID: 33585414 PMCID: PMC7873862 DOI: 10.3389/fbioe.2020.612832] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 12/04/2020] [Indexed: 01/11/2023] Open
Abstract
An oleaginous yeast Rhodosporidium toruloides is a promising host for converting lignocellulosic biomass to bioproducts and biofuels. In this work, we performed multi-omics analysis of lignocellulosic carbon utilization in R. toruloides and reconstructed the genome-scale metabolic network of R. toruloides. High-quality metabolic network models for model organisms and orthologous protein mapping were used to build a draft metabolic network reconstruction. The reconstruction was manually curated to build a metabolic model using functional annotation and multi-omics data including transcriptomics, proteomics, metabolomics, and RB-TDNA sequencing. The multi-omics data and metabolic model were used to investigate R. toruloides metabolism including lipid accumulation and lignocellulosic carbon utilization. The developed metabolic model was validated against high-throughput growth phenotyping and gene fitness data, and further refined to resolve the inconsistencies between prediction and data. We believe that this is the most complete and accurate metabolic network model available for R. toruloides to date.
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Affiliation(s)
- Joonhoon Kim
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,Department of Energy, Joint BioEnergy Institute, Emeryville, CA, United States.,Pacific Northwest National Laboratory, Richland, WA, United States
| | - Samuel T Coradetti
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,Sandia National Laboratories, Livermore, CA, United States
| | - Young-Mo Kim
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,Pacific Northwest National Laboratory, Richland, WA, United States
| | - Yuqian Gao
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,Pacific Northwest National Laboratory, Richland, WA, United States
| | - Junko Yaegashi
- Department of Energy, Joint BioEnergy Institute, Emeryville, CA, United States.,Pacific Northwest National Laboratory, Richland, WA, United States
| | - Jeremy D Zucker
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,Pacific Northwest National Laboratory, Richland, WA, United States
| | - Nathalie Munoz
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,Pacific Northwest National Laboratory, Richland, WA, United States
| | - Erika M Zink
- Pacific Northwest National Laboratory, Richland, WA, United States
| | - Kristin E Burnum-Johnson
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,Pacific Northwest National Laboratory, Richland, WA, United States
| | - Scott E Baker
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,Department of Energy, Joint BioEnergy Institute, Emeryville, CA, United States.,Pacific Northwest National Laboratory, Richland, WA, United States
| | - Blake A Simmons
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,Department of Energy, Joint BioEnergy Institute, Emeryville, CA, United States.,Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Jeffrey M Skerker
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, United States
| | - John M Gladden
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,Department of Energy, Joint BioEnergy Institute, Emeryville, CA, United States.,Sandia National Laboratories, Livermore, CA, United States
| | - Jon K Magnuson
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,Department of Energy, Joint BioEnergy Institute, Emeryville, CA, United States.,Pacific Northwest National Laboratory, Richland, WA, United States
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15
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Abstract
Pathway localization by fluorophore or epitope tagging can be accomplished through a multi-staged DNA construct and confirmation process, to generate a series of successfully tagged protein targets. Prerequisite conditions for this process in Y. lipolytica are auxotrophic selection (leu2 or ura3), impaired non-homologous end joining by deletion or impairment of ku70, and plasmids or gene pieces for epitope-selection cassette construction. The general approach for gene tagging can work for C- or N-terminal tags. Gene overexpression from an episomal plasmid can be accomplished through transcript amplification and cloning. C-terminal tagging allows expression of a gene-GFP fusion to be regulated from the endogenous promoter. The epitope-selection cassette also includes a constitutive or highly expressed promoter driving the auxotrophic or other selectable marker gene such as one conferring antifungal or antibiotic resistance. Strains for pathway localization utilize overlap PCR, PEG-based transformation, and a fast DNA preparation for rapid colony screening. Successful transformants can be used for pathway localization and condition-specific response analysis.
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Affiliation(s)
- Erin L Bredeweg
- Environmental and Molecular Sciences Laboratory, PNNL, Richland, WA, USA
| | - Scott E Baker
- Environmental and Molecular Sciences Laboratory, PNNL, Richland, WA, USA.
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16
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Ferrara M, Gallo A, Perrone G, Magistà D, Baker SE. Comparative Genomic Analysis of Ochratoxin A Biosynthetic Cluster in Producing Fungi: New Evidence of a Cyclase Gene Involvement. Front Microbiol 2020; 11:581309. [PMID: 33391201 PMCID: PMC7775548 DOI: 10.3389/fmicb.2020.581309] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 11/30/2020] [Indexed: 12/13/2022] Open
Abstract
The widespread use of Next-Generation Sequencing has opened a new era in the study of biological systems by significantly increasing the catalog of fungal genomes sequences and identifying gene clusters for known secondary metabolites as well as novel cryptic ones. However, most of these clusters still need to be examined in detail to completely understand the pathway steps and the regulation of the biosynthesis of metabolites. Genome sequencing approach led to the identification of the biosynthetic genes cluster of ochratoxin A (OTA) in a number of producing fungal species. Ochratoxin A is a potent pentaketide nephrotoxin produced by Aspergillus and Penicillium species and found as widely contaminant in food, beverages and feed. The increasing availability of several new genome sequences of OTA producer species in JGI Mycocosm and/or GenBank databanks led us to analyze and update the gene cluster structure in 19 Aspergillus and 2 Penicillium OTA producing species, resulting in a well conserved organization of OTA core genes among the species. Furthermore, our comparative genome analyses evidenced the presence of an additional gene, previously undescribed, located between the polyketide and non-ribosomal synthase genes in the cluster of all the species analyzed. The presence of a SnoaL cyclase domain in the sequence of this gene supports its putative role in the polyketide cyclization reaction during the initial steps of the OTA biosynthesis pathway. The phylogenetic analysis showed a clustering of OTA SnoaL domains in accordance with the phylogeny of OTA producing species at species and section levels. The characterization of this new OTA gene, its putative role and its expression evidence in three important representative producing species, are reported here for the first time.
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Affiliation(s)
- Massimo Ferrara
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Bari, Italy
| | - Antonia Gallo
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Lecce, Italy
| | - Giancarlo Perrone
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Bari, Italy
| | - Donato Magistà
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Bari, Italy
| | - Scott E Baker
- Functional and Systems Biology Group, Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States.,DOE Joint Bioenergy Institute, Emeryville, CA, United States
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17
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Affiliation(s)
- Scott E. Baker
- Joint BioEnergy Institute, Emeryville, CA, United States
- Functional and Systems Biology Group, Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
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18
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Gao Y, Fillmore TL, Munoz N, Bentley GJ, Johnson CW, Kim J, Meadows JA, Zucker JD, Burnet MC, Lipton AK, Bilbao A, Orton DJ, Kim YM, Moore RJ, Robinson EW, Baker SE, Webb-Robertson BJM, Guss AM, Gladden JM, Beckham GT, Magnuson JK, Burnum-Johnson KE. High-Throughput Large-Scale Targeted Proteomics Assays for Quantifying Pathway Proteins in Pseudomonas putida KT2440. Front Bioeng Biotechnol 2020; 8:603488. [PMID: 33425868 PMCID: PMC7793925 DOI: 10.3389/fbioe.2020.603488] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 11/10/2020] [Indexed: 11/13/2022] Open
Abstract
Targeted proteomics is a mass spectrometry-based protein quantification technique with high sensitivity, accuracy, and reproducibility. As a key component in the multi-omics toolbox of systems biology, targeted liquid chromatography-selected reaction monitoring (LC-SRM) measurements are critical for enzyme and pathway identification and design in metabolic engineering. To fulfill the increasing need for analyzing large sample sets with faster turnaround time in systems biology, high-throughput LC-SRM is greatly needed. Even though nanoflow LC-SRM has better sensitivity, it lacks the speed offered by microflow LC-SRM. Recent advancements in mass spectrometry instrumentation significantly enhance the scan speed and sensitivity of LC-SRM, thereby creating opportunities for applying the high speed of microflow LC-SRM without losing peptide multiplexing power or sacrificing sensitivity. Here, we studied the performance of microflow LC-SRM relative to nanoflow LC-SRM by monitoring 339 peptides representing 132 enzymes in Pseudomonas putida KT2440 grown on various carbon sources. The results from the two LC-SRM platforms are highly correlated. In addition, the response curve study of 248 peptides demonstrates that microflow LC-SRM has comparable sensitivity for the majority of detected peptides and better mass spectrometry signal and chromatography stability than nanoflow LC-SRM.
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Affiliation(s)
- Yuqian Gao
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,Pacific Northwest National Laboratory, Richland, WA, United States
| | | | - Nathalie Munoz
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,Pacific Northwest National Laboratory, Richland, WA, United States
| | - Gayle J Bentley
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,National Renewable Energy Laboratory, Golden, CO, United States
| | - Christopher W Johnson
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,National Renewable Energy Laboratory, Golden, CO, United States
| | - Joonhoon Kim
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,Pacific Northwest National Laboratory, Richland, WA, United States
| | - Jamie A Meadows
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,Sandia National Laboratories, Livermore, CA, United States
| | - Jeremy D Zucker
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,Pacific Northwest National Laboratory, Richland, WA, United States
| | - Meagan C Burnet
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,Pacific Northwest National Laboratory, Richland, WA, United States
| | - Anna K Lipton
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,Pacific Northwest National Laboratory, Richland, WA, United States
| | - Aivett Bilbao
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,Pacific Northwest National Laboratory, Richland, WA, United States
| | - Daniel J Orton
- Pacific Northwest National Laboratory, Richland, WA, United States
| | - Young-Mo Kim
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,Pacific Northwest National Laboratory, Richland, WA, United States
| | - Ronald J Moore
- Pacific Northwest National Laboratory, Richland, WA, United States
| | - Errol W Robinson
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,Pacific Northwest National Laboratory, Richland, WA, United States
| | - Scott E Baker
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,Pacific Northwest National Laboratory, Richland, WA, United States
| | - Bobbie-Jo M Webb-Robertson
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,Pacific Northwest National Laboratory, Richland, WA, United States
| | - Adam M Guss
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - John M Gladden
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,Sandia National Laboratories, Livermore, CA, United States
| | - Gregg T Beckham
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,National Renewable Energy Laboratory, Golden, CO, United States
| | - Jon K Magnuson
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,Pacific Northwest National Laboratory, Richland, WA, United States
| | - Kristin E Burnum-Johnson
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States.,Pacific Northwest National Laboratory, Richland, WA, United States
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19
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Subedi NR, Jung PS, Bredeweg EL, Nemati S, Baker SE, Christodoulides DN, Vasdekis AE. Integrative quantitative-phase and airy light-sheet imaging. Sci Rep 2020; 10:20150. [PMID: 33214600 PMCID: PMC7678854 DOI: 10.1038/s41598-020-76730-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 10/30/2020] [Indexed: 01/05/2023] Open
Abstract
Light-sheet microscopy enables considerable speed and phototoxicity gains, while quantitative-phase imaging confers label-free recognition of cells and organelles, and quantifies their number-density that, thermodynamically, is more representative of metabolism than size. Here, we report the fusion of these two imaging modalities onto a standard inverted microscope that retains compatibility with microfluidics and open-source software for image acquisition and processing. An accelerating Airy-beam light-sheet critically enabled imaging areas that were greater by more than one order of magnitude than a Gaussian beam illumination and matched exactly those of quantitative-phase imaging. Using this integrative imaging system, we performed a demonstrative multivariate investigation of live-cells in microfluidics that unmasked that cellular noise can affect the compartmental localization of metabolic reactions. We detail the design, assembly, and performance of the integrative imaging system, and discuss potential applications in biotechnology and evolutionary biology.
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Affiliation(s)
- N R Subedi
- Department of Physics, University of Idaho, Moscow, ID, 83844, USA
| | - P S Jung
- CREOL-The College of Optics and Photonics, University of Central Florida, Orlando, FL, 32816-2700, USA
- Faculty of Physics, Warsaw University of Technology, Warsaw, Poland
| | - E L Bredeweg
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - S Nemati
- Department of Physics, University of Idaho, Moscow, ID, 83844, USA
| | - S E Baker
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - D N Christodoulides
- CREOL-The College of Optics and Photonics, University of Central Florida, Orlando, FL, 32816-2700, USA
| | - A E Vasdekis
- Department of Physics, University of Idaho, Moscow, ID, 83844, USA.
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20
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Daly P, Peng M, Mitchell HD, Kim Y, Ansong C, Brewer H, de Gijsel P, Lipton MS, Markillie LM, Nicora CD, Orr G, Wiebenga A, Hildén KS, Kabel MA, Baker SE, Mäkelä MR, de Vries RP. Colonies of the fungus Aspergillus niger are highly differentiated to adapt to local carbon source variation. Environ Microbiol 2020; 22:1154-1166. [PMID: 31876091 PMCID: PMC7065180 DOI: 10.1111/1462-2920.14907] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 12/20/2019] [Indexed: 11/27/2022]
Abstract
Saprobic fungi, such as Aspergillus niger, grow as colonies consisting of a network of branching and fusing hyphae that are often considered to be relatively uniform entities in which nutrients can freely move through the hyphae. In nature, different parts of a colony are often exposed to different nutrients. We have investigated, using a multi-omics approach, adaptation of A. niger colonies to spatially separated and compositionally different plant biomass substrates. This demonstrated a high level of intra-colony differentiation, which closely matched the locally available substrate. The part of the colony exposed to pectin-rich sugar beet pulp and to xylan-rich wheat bran showed high pectinolytic and high xylanolytic transcript and protein levels respectively. This study therefore exemplifies the high ability of fungal colonies to differentiate and adapt to local conditions, ensuring efficient use of the available nutrients, rather than maintaining a uniform physiology throughout the colony.
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Affiliation(s)
- Paul Daly
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular PhysiologyUtrecht UniversityUppsalalaan 8, 3584 CT UtrechtThe Netherlands
| | - Mao Peng
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular PhysiologyUtrecht UniversityUppsalalaan 8, 3584 CT UtrechtThe Netherlands
| | - Hugh D. Mitchell
- Biological Sciences DivisionsPacific Northwest National LaboratoryRichlandWA99352USA
| | - Young‐Mo Kim
- Biological Sciences DivisionsPacific Northwest National LaboratoryRichlandWA99352USA
| | - Charles Ansong
- Biological Sciences DivisionsPacific Northwest National LaboratoryRichlandWA99352USA
| | - Heather Brewer
- Environmental Molecular Sciences LaboratoryPacific Northwest National LaboratoryRichlandWA99352USA
| | - Peter de Gijsel
- Laboratory of Food ChemistryWageningen UniversityBornse Weilanden 9, 6708 WG WageningenThe Netherlands
| | - Mary S. Lipton
- Environmental Molecular Sciences LaboratoryPacific Northwest National LaboratoryRichlandWA99352USA
| | - Lye Meng Markillie
- Biological Sciences DivisionsPacific Northwest National LaboratoryRichlandWA99352USA
| | - Carrie D. Nicora
- Biological Sciences DivisionsPacific Northwest National LaboratoryRichlandWA99352USA
| | - Galya Orr
- Environmental Molecular Sciences LaboratoryPacific Northwest National LaboratoryRichlandWA99352USA
| | - Ad Wiebenga
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular PhysiologyUtrecht UniversityUppsalalaan 8, 3584 CT UtrechtThe Netherlands
| | - Kristiina S. Hildén
- Department of MicrobiologyUniversity of HelsinkiViikinkaari 9, 00790 HelsinkiFinland
| | - Mirjam A. Kabel
- Laboratory of Food ChemistryWageningen UniversityBornse Weilanden 9, 6708 WG WageningenThe Netherlands
| | - Scott E. Baker
- Environmental Molecular Sciences LaboratoryPacific Northwest National LaboratoryRichlandWA99352USA
| | - Miia R. Mäkelä
- Department of MicrobiologyUniversity of HelsinkiViikinkaari 9, 00790 HelsinkiFinland
| | - Ronald P. de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular PhysiologyUtrecht UniversityUppsalalaan 8, 3584 CT UtrechtThe Netherlands
- Department of MicrobiologyUniversity of HelsinkiViikinkaari 9, 00790 HelsinkiFinland
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21
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Haridas S, Albert R, Binder M, Bloem J, LaButti K, Salamov A, Andreopoulos B, Baker SE, Barry K, Bills G, Bluhm BH, Cannon C, Castanera R, Culley DE, Daum C, Ezra D, González JB, Henrissat B, Kuo A, Liang C, Lipzen A, Lutzoni F, Magnuson J, Mondo SJ, Nolan M, Ohm RA, Pangilinan J, Park HJ, Ramírez L, Alfaro M, Sun H, Tritt A, Yoshinaga Y, Zwiers LH, Turgeon BG, Goodwin SB, Spatafora JW, Crous PW, Grigoriev IV. 101 Dothideomycetes genomes: A test case for predicting lifestyles and emergence of pathogens. Stud Mycol 2020; 96:141-153. [PMID: 32206138 PMCID: PMC7082219 DOI: 10.1016/j.simyco.2020.01.003] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Dothideomycetes is the largest class of kingdom Fungi and comprises an incredible diversity of lifestyles, many of which have evolved multiple times. Plant pathogens represent a major ecological niche of the class Dothideomycetes and they are known to infect most major food crops and feedstocks for biomass and biofuel production. Studying the ecology and evolution of Dothideomycetes has significant implications for our fundamental understanding of fungal evolution, their adaptation to stress and host specificity, and practical implications with regard to the effects of climate change and on the food, feed, and livestock elements of the agro-economy. In this study, we present the first large-scale, whole-genome comparison of 101 Dothideomycetes introducing 55 newly sequenced species. The availability of whole-genome data produced a high-confidence phylogeny leading to reclassification of 25 organisms, provided a clearer picture of the relationships among the various families, and indicated that pathogenicity evolved multiple times within this class. We also identified gene family expansions and contractions across the Dothideomycetes phylogeny linked to ecological niches providing insights into genome evolution and adaptation across this group. Using machine-learning methods we classified fungi into lifestyle classes with >95 % accuracy and identified a small number of gene families that positively correlated with these distinctions. This can become a valuable tool for genome-based prediction of species lifestyle, especially for rarely seen and poorly studied species.
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Key Words
- Aulographales Crous, Spatafora, Haridas & Grigoriev
- Coniosporiaceae Crous, Spatafora, Haridas & Grigoriev
- Coniosporiales Crous, Spatafora, Haridas & Grigoriev
- Eremomycetales Crous, Spatafora, Haridas & Grigoriev
- Fungal evolution
- Genome-based prediction
- Lineolataceae Crous, Spatafora, Haridas & Grigoriev
- Lineolatales Crous, Spatafora, Haridas & Grigoriev
- Machine-learning
- New taxa
- Rhizodiscinaceae Crous, Spatafora, Haridas & Grigoriev
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Affiliation(s)
- S Haridas
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - R Albert
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - M Binder
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - J Bloem
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - K LaButti
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - A Salamov
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - B Andreopoulos
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - S E Baker
- Functional and Systems Biology Group, Environmental Molecular Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - K Barry
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - G Bills
- University of Texas Health Science Center, Houston, TX, USA
| | - B H Bluhm
- University of Arkansas, Fayelletville, AR, USA
| | - C Cannon
- Texas Tech University, Lubbock, TX, USA
| | - R Castanera
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Institute for Multidisciplinary Research in Applied Biology (IMAB-UPNA), Universidad Pública de Navarra, Pamplona, Navarra, Spain
| | - D E Culley
- Functional and Systems Biology Group, Environmental Molecular Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - C Daum
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - D Ezra
- Agricultural Research Organization, Volcani Center, Rishon LeTsiyon, Israel
| | - J B González
- Section of Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - B Henrissat
- CNRS, Aix-Marseille Université, Marseille, France.,INRA, Marseille, France.,Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - A Kuo
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - C Liang
- College of Agronomy and Plant Protection, Qingdao Agricultural University, China
| | - A Lipzen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - F Lutzoni
- Department of Biology, Duke University, Durham, NC, USA
| | - J Magnuson
- Functional and Systems Biology Group, Environmental Molecular Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - S J Mondo
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Bioagricultural Science and Pest Management Department, Colorado State University, Fort Collins, CO, USA
| | - M Nolan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - R A Ohm
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Microbiology, Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - J Pangilinan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - H-J Park
- Section of Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - L Ramírez
- Institute for Multidisciplinary Research in Applied Biology (IMAB-UPNA), Universidad Pública de Navarra, Pamplona, Navarra, Spain
| | - M Alfaro
- Institute for Multidisciplinary Research in Applied Biology (IMAB-UPNA), Universidad Pública de Navarra, Pamplona, Navarra, Spain
| | - H Sun
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - A Tritt
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Y Yoshinaga
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - L-H Zwiers
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - B G Turgeon
- Section of Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - S B Goodwin
- U.S. Department of Agriculture-Agricultural Research Service, 915 W. State Street, West Lafayette, IN, USA
| | - J W Spatafora
- Department of Botany & Plant Pathology, Oregon State University, Oregon State University, Corvallis, OR, USA
| | - P W Crous
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,Microbiology, Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - I V Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
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22
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Leynaud-Kieffer LMC, Curran SC, Kim I, Magnuson JK, Gladden JM, Baker SE, Simmons BA. A new approach to Cas9-based genome editing in Aspergillus niger that is precise, efficient and selectable. PLoS One 2019; 14:e0210243. [PMID: 30653574 PMCID: PMC6336261 DOI: 10.1371/journal.pone.0210243] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 12/19/2018] [Indexed: 02/06/2023] Open
Abstract
Aspergillus niger and other filamentous fungi are widely used in industry, but efficient genetic engineering of these hosts remains nascent. For example, while molecular genetic tools have been developed, including CRISPR/Cas9, facile genome engineering of A. niger remains challenging. To address these challenges, we have developed a simple Cas9-based gene targeting method that provides selectable, iterative, and ultimately marker-free generation of genomic deletions and insertions. This method leverages locus-specific “pop-out” recombination to suppress off-target integrations. We demonstrated the effectiveness of this method by targeting the phenotypic marker albA and validated it by targeting the glaA and mstC loci. After two selection steps, we observed 100% gene editing efficiency across all three loci. This method greatly reduces the effort required to engineer the A. niger genome and overcomes low Cas9 transformations efficiency by eliminating the need for extensive screening. This method represents a significant addition to the A. niger genome engineering toolbox and could be adapted for use in other organisms. It is expected that this method will impact several areas of industrial biotechnology, such as the development of new strains for the secretion of heterologous enzymes and the discovery and optimization of metabolic pathways.
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Affiliation(s)
- Laure M. C. Leynaud-Kieffer
- Swiss Federal Institute of Technology Lausanne, Lausanne, Vaud, Switzerland
- Joint Bioenergy Institute, Emeryville, CA, United States of America
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America
| | - Samuel C. Curran
- Joint Bioenergy Institute, Emeryville, CA, United States of America
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America
- Comparative Biochemistry Graduate Group, University of California Berkeley, Berkeley, CA, United States of America
| | - Irene Kim
- Department of Chemistry, University of California, Berkeley, CA, United States of America
| | - Jon K. Magnuson
- Joint Bioenergy Institute, Emeryville, CA, United States of America
- Chemical and Biological Process Development Group, Pacific Northwest National Laboratory, Richland, WA, United States of America
| | - John M. Gladden
- Joint Bioenergy Institute, Emeryville, CA, United States of America
- Department of Biomass Science and Conversion Technology, Sandia National Laboratories, Livermore, CA, United States of America
| | - Scott E. Baker
- Joint Bioenergy Institute, Emeryville, CA, United States of America
- Biosystems Design and Simulation Group, Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States of America
| | - Blake A. Simmons
- Joint Bioenergy Institute, Emeryville, CA, United States of America
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America
- * E-mail:
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23
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Vesth TC, Nybo JL, Theobald S, Frisvad JC, Larsen TO, Nielsen KF, Hoof JB, Brandl J, Salamov A, Riley R, Gladden JM, Phatale P, Nielsen MT, Lyhne EK, Kogle ME, Strasser K, McDonnell E, Barry K, Clum A, Chen C, LaButti K, Haridas S, Nolan M, Sandor L, Kuo A, Lipzen A, Hainaut M, Drula E, Tsang A, Magnuson JK, Henrissat B, Wiebenga A, Simmons BA, Mäkelä MR, de Vries RP, Grigoriev IV, Mortensen UH, Baker SE, Andersen MR. Investigation of inter- and intraspecies variation through genome sequencing of Aspergillus section Nigri. Nat Genet 2018; 50:1688-1695. [PMID: 30349117 DOI: 10.1038/s41588-018-0246-1] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 08/23/2018] [Indexed: 01/27/2023]
Abstract
Aspergillus section Nigri comprises filamentous fungi relevant to biomedicine, bioenergy, health, and biotechnology. To learn more about what genetically sets these species apart, as well as about potential applications in biotechnology and biomedicine, we sequenced 23 genomes de novo, forming a full genome compendium for the section (26 species), as well as 6 Aspergillus niger isolates. This allowed us to quantify both inter- and intraspecies genomic variation. We further predicted 17,903 carbohydrate-active enzymes and 2,717 secondary metabolite gene clusters, which we condensed into 455 distinct families corresponding to compound classes, 49% of which are only found in single species. We performed metabolomics and genetic engineering to correlate genotypes to phenotypes, as demonstrated for the metabolite aurasperone, and by heterologous transfer of citrate production to Aspergillus nidulans. Experimental and computational analyses showed that both secondary metabolism and regulation are key factors that are significant in the delineation of Aspergillus species.
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Affiliation(s)
- Tammi C Vesth
- Department of Biotechnology and Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Jane L Nybo
- Department of Biotechnology and Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Sebastian Theobald
- Department of Biotechnology and Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Jens C Frisvad
- Department of Biotechnology and Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Thomas O Larsen
- Department of Biotechnology and Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Kristian F Nielsen
- Department of Biotechnology and Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Jakob B Hoof
- Department of Biotechnology and Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Julian Brandl
- Department of Biotechnology and Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Asaf Salamov
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Robert Riley
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.,Amyris, Inc., Emeryville, CA, USA
| | - John M Gladden
- US Department of Energy Joint BioEnergy Institute, Emeryville, CA, USA.,Sandia National Laboratory, Livermore, CA, USA
| | - Pallavi Phatale
- US Department of Energy Joint BioEnergy Institute, Emeryville, CA, USA.,Chemical and Biological Process Development Group, Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Morten T Nielsen
- Department of Biotechnology and Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Ellen K Lyhne
- Department of Biotechnology and Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Martin E Kogle
- Department of Biotechnology and Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Kimchi Strasser
- Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada
| | - Erin McDonnell
- Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Alicia Clum
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Cindy Chen
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Kurt LaButti
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Sajeet Haridas
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Matt Nolan
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Laura Sandor
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Alan Kuo
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Matthieu Hainaut
- Architecture et Fonction des Macromolécules Biologiques, CNRS UMR 7257, Aix-Marseille University, Marseille, France.,Institut National de la Recherche Agronomique, USC 1408 Architecture et Fonction des Macromolécules Biologiques, Marseille, France
| | - Elodie Drula
- Architecture et Fonction des Macromolécules Biologiques, CNRS UMR 7257, Aix-Marseille University, Marseille, France.,Institut National de la Recherche Agronomique, USC 1408 Architecture et Fonction des Macromolécules Biologiques, Marseille, France
| | - Adrian Tsang
- Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada
| | - Jon K Magnuson
- US Department of Energy Joint BioEnergy Institute, Emeryville, CA, USA.,Chemical and Biological Process Development Group, Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS UMR 7257, Aix-Marseille University, Marseille, France.,Institut National de la Recherche Agronomique, USC 1408 Architecture et Fonction des Macromolécules Biologiques, Marseille, France.,Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ad Wiebenga
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute and Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands
| | - Blake A Simmons
- US Department of Energy Joint BioEnergy Institute, Emeryville, CA, USA.,Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Miia R Mäkelä
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute and Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands.,Department of Microbiology, University of Helsinki, Helsinki, Finland
| | - Ronald P de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute and Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.,Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Uffe H Mortensen
- Department of Biotechnology and Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Scott E Baker
- US Department of Energy Joint BioEnergy Institute, Emeryville, CA, USA. .,Environmental Molecular Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.
| | - Mikael R Andersen
- Department of Biotechnology and Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark.
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24
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Daly P, López SC, Peng M, Lancefield CS, Purvine SO, Kim Y, Zink EM, Dohnalkova A, Singan VR, Lipzen A, Dilworth D, Wang M, Ng V, Robinson E, Orr G, Baker SE, Bruijnincx PCA, Hildén KS, Grigoriev IV, Mäkelä MR, de Vries RP. Dichomitus squalens
partially tailors its molecular responses to the composition of solid wood. Environ Microbiol 2018; 20:4141-4156. [DOI: 10.1111/1462-2920.14416] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 09/11/2018] [Accepted: 09/13/2018] [Indexed: 12/23/2022]
Affiliation(s)
- Paul Daly
- Fungal Physiology Westerdijk Fungal Biodiversity Institute and Fungal Molecular Physiology, Utrecht University Utrecht The Netherlands
| | - Sara Casado López
- Fungal Physiology Westerdijk Fungal Biodiversity Institute and Fungal Molecular Physiology, Utrecht University Utrecht The Netherlands
| | - Mao Peng
- Fungal Physiology Westerdijk Fungal Biodiversity Institute and Fungal Molecular Physiology, Utrecht University Utrecht The Netherlands
| | - Christopher S. Lancefield
- Inorganic Chemistry and Catalysis, Debye Institute for Nanomaterials Science Utrecht University Utrecht The Netherlands
| | - Samuel O. Purvine
- Environmental Molecular Sciences Laboratory Pacific Northwest National Laboratory Richland WA USA
| | - Young‐Mo Kim
- Biological Sciences Division Pacific Northwest National Laboratory Richland WA USA
| | - Erika M. Zink
- Biological Sciences Division Pacific Northwest National Laboratory Richland WA USA
| | - Alice Dohnalkova
- Environmental Molecular Sciences Laboratory Pacific Northwest National Laboratory Richland WA USA
| | | | - Anna Lipzen
- US Department of Energy Joint Genome Institute Walnut Creek CA USA
| | - David Dilworth
- US Department of Energy Joint Genome Institute Walnut Creek CA USA
| | - Mei Wang
- US Department of Energy Joint Genome Institute Walnut Creek CA USA
| | - Vivian Ng
- US Department of Energy Joint Genome Institute Walnut Creek CA USA
| | - Errol Robinson
- Environmental Molecular Sciences Laboratory Pacific Northwest National Laboratory Richland WA USA
| | - Galya Orr
- Environmental Molecular Sciences Laboratory Pacific Northwest National Laboratory Richland WA USA
| | - Scott E. Baker
- Environmental Molecular Sciences Laboratory Pacific Northwest National Laboratory Richland WA USA
| | - Pieter C. A. Bruijnincx
- Inorganic Chemistry and Catalysis, Debye Institute for Nanomaterials Science Utrecht University Utrecht The Netherlands
| | | | | | - Miia R. Mäkelä
- Department of Microbiology University of Helsinki Helsinki Finland
| | - Ronald P. de Vries
- Fungal Physiology Westerdijk Fungal Biodiversity Institute and Fungal Molecular Physiology, Utrecht University Utrecht The Netherlands
- Department of Microbiology University of Helsinki Helsinki Finland
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25
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Abstract
The secretion of enzymes used by fungi to digest their environment has been exploited by humans for centuries for food and beverage production. More than a century after the first biotechnology patent, we know that the enzyme cocktails secreted by these amazing organisms have tremendous use across a number of industrial processes. Secreting the maximum titer of enzymes is critical to the economic feasibility of these processes. Traditional mutagenesis and screening approaches have generated the vast majority of strains used by industry for the production of enzymes. Until the emergence of economical next generation DNA sequencing platforms, the majority of the genes mutated in these screens remained uncharacterized at the sequence level. In addition, mutagenesis comes with a cost to an organism’s fitness, making tractable rational strain design approaches an attractive alternative. As an alternative to traditional mutagenesis and screening, controlled manipulation of multiple genes involved in processes that impact the ability of a fungus to sense its environment, regulate transcription of enzyme-encoding genes, and efficiently secrete these proteins will allow for rational design of improved fungal protein production strains.
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Affiliation(s)
- Scott E Baker
- Department of Energy Joint BioEnergy Institute, Emeryville, CA, 94608, USA.
- Biosystems Design and Simulation Group, Environmental Molecular Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
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26
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Cannon WR, Zucker JD, Baxter DJ, Kumar N, Baker SE, Hurley JM, Dunlap JC. Prediction of Metabolite Concentrations, Rate Constants and Post-Translational Regulation Using Maximum Entropy-Based Simulations with Application to Central Metabolism of Neurospora crassa. Processes (Basel) 2018; 6. [PMID: 33824861 PMCID: PMC8020867 DOI: 10.3390/pr6060063] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
We report the application of a recently proposed approach for modeling biological systems using a maximum entropy production rate principle in lieu of having in vivo rate constants. The method is applied in four steps: (1) a new ordinary differential equation (ODE) based optimization approach based on Marcelin’s 1910 mass action equation is used to obtain the maximum entropy distribution; (2) the predicted metabolite concentrations are compared to those generally expected from experiments using a loss function from which post-translational regulation of enzymes is inferred; (3) the system is re-optimized with the inferred regulation from which rate constants are determined from the metabolite concentrations and reaction fluxes; and finally (4) a full ODE-based, mass action simulation with rate parameters and allosteric regulation is obtained. From the last step, the power characteristics and resistance of each reaction can be determined. The method is applied to the central metabolism of Neurospora crassa and the flow of material through the three competing pathways of upper glycolysis, the non-oxidative pentose phosphate pathway, and the oxidative pentose phosphate pathway are evaluated as a function of the NADP/NADPH ratio. It is predicted that regulation of phosphofructokinase (PFK) and flow through the pentose phosphate pathway are essential for preventing an extreme level of fructose 1,6-bisphophate accumulation. Such an extreme level of fructose 1,6-bisphophate would otherwise result in a glassy cytoplasm with limited diffusion, dramatically decreasing the entropy and energy production rate and, consequently, biological competitiveness.
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Affiliation(s)
- William R. Cannon
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
- Correspondence: ; Tel.: +1-509-375-6732
| | - Jeremy D. Zucker
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Douglas J. Baxter
- Research Computing Group, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Neeraj Kumar
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Scott E. Baker
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Jennifer M. Hurley
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Jay C. Dunlap
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
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27
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Khosravi C, Battaglia E, Kun RS, Dalhuijsen S, Visser J, Aguilar-Pontes MV, Zhou M, Heyman HM, Kim YM, Baker SE, de Vries RP. Blocking hexose entry into glycolysis activates alternative metabolic conversion of these sugars and upregulates pentose metabolism in Aspergillus nidulans. BMC Genomics 2018; 19:214. [PMID: 29566661 PMCID: PMC5863803 DOI: 10.1186/s12864-018-4609-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 03/19/2018] [Indexed: 11/11/2022] Open
Abstract
Background Plant biomass is the most abundant carbon source for many fungal species. In the biobased industry fungi, are used to produce lignocellulolytic enzymes to degrade agricultural waste biomass. Here we evaluated if it would be possible to create an Aspergillus nidulans strain that releases, but does not metabolize hexoses from plant biomass. For this purpose, metabolic mutants were generated that were impaired in glycolysis, by using hexokinase (hxkA) and glucokinase (glkA) negative strains. To prevent repression of enzyme production due to the hexose accumulation, strains were generated that combined these mutations with a deletion in creA, the repressor involved in regulating preferential use of different carbon catabolic pathways. Results Phenotypic analysis revealed reduced growth for the hxkA1 glkA4 mutant on wheat bran. However, hexoses did not accumulate during growth of the mutants on wheat bran, suggesting that glucose metabolism is re-routed towards alternative carbon catabolic pathways. The creAΔ4 mutation in combination with preventing initial phosphorylation in glycolysis resulted in better growth than the hxkA/glkA mutant and an increased expression of pentose catabolic and pentose phosphate pathway genes. This indicates that the reduced ability to use hexoses as carbon sources created a shift towards the pentose fraction of wheat bran as a major carbon source to support growth. Conclusion Blocking the direct entry of hexoses to glycolysis activates alternative metabolic conversion of these sugars in A. nidulans during growth on plant biomass, but also upregulates conversion of other sugars, such as pentoses. Electronic supplementary material The online version of this article (10.1186/s12864-018-4609-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Claire Khosravi
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands
| | - Evy Battaglia
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands
| | - Roland S Kun
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands
| | - Sacha Dalhuijsen
- Microbiology, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands
| | - Jaap Visser
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands.,Fungal Genetics and Technology Consultancy, P.O. Box 396, 6700, AJ, Wageningen, The Netherlands
| | - María Victoria Aguilar-Pontes
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands
| | - Miaomiao Zhou
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands
| | - Heino M Heyman
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Young-Mo Kim
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Scott E Baker
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Ronald P de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands. .,Microbiology, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands.
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28
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Reilly MC, Kim J, Lynn J, Simmons BA, Gladden JM, Magnuson JK, Baker SE. Forward genetics screen coupled with whole-genome resequencing identifies novel gene targets for improving heterologous enzyme production in Aspergillus niger. Appl Microbiol Biotechnol 2018; 102:1797-1807. [PMID: 29305699 PMCID: PMC5794824 DOI: 10.1007/s00253-017-8717-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 12/11/2017] [Accepted: 12/12/2017] [Indexed: 12/12/2022]
Abstract
Plant biomass, once reduced to its composite sugars, can be converted to fuel substitutes. One means of overcoming the recalcitrance of lignocellulose is pretreatment followed by enzymatic hydrolysis. However, currently available commercial enzyme cocktails are inhibited in the presence of residual pretreatment chemicals. Recent studies have identified a number of cellulolytic enzymes from bacteria that are tolerant to pretreatment chemicals such as ionic liquids. The challenge now is generation of these enzymes in copious amounts, an arena where fungal organisms such as Aspergillus niger have proven efficient. Fungal host strains still need to be engineered to increase production titers of heterologous protein over native enzymes, which has been a difficult task. Here, we developed a forward genetics screen coupled with whole-genome resequencing to identify specific lesions responsible for a protein hyper-production phenotype in A. niger. This strategy successfully identified novel targets, including a low-affinity glucose transporter, MstC, whose deletion significantly improved secretion of recombinant proteins driven by a glucoamylase promoter.
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Affiliation(s)
- Morgann C Reilly
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Chemical and Biological Processes Development Group, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Joonhoon Kim
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Chemical and Biological Processes Development Group, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Jed Lynn
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Naval Medical Research Unit Dayton, Wright-Patterson Air Force Base, Dayton, OH, 45433, USA
| | - Blake A Simmons
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - John M Gladden
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Biomass Science and Conversion Technologies Department, Sandia National Laboratories, Livermore, CA, 94551, USA
| | - Jon K Magnuson
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Chemical and Biological Processes Development Group, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Scott E Baker
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA. .,Biosystems Design and Simulation Group, Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
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29
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Reilly MC, Amaike Campen S, Simmons BA, Baker SE, Gladden JM, Magnuson JK. Correction to: Cloning and Expression of Heterologous Cellulases and Enzymes in Aspergillus niger. Methods Mol Biol 2018; 1796:E1. [PMID: 30374680 DOI: 10.1007/978-1-4939-7877-9_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The author's family name were incorrectly published in the original version. This has been corrected to read as.
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Affiliation(s)
- Morgann C Reilly
- Joint BioEnergy Institute, Emeryville, CA, USA
- University of California, San Francisco, CA, USA
| | - Saori Amaike Campen
- Joint BioEnergy Institute, Emeryville, CA, USA
- J. Craig Venter Institute, San Diego, CA, USA
| | - Blake A Simmons
- Joint BioEnergy Institute, Emeryville, CA, USA
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Scott E Baker
- Joint BioEnergy Institute, Emeryville, CA, USA
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - John M Gladden
- Joint BioEnergy Institute, Emeryville, CA, USA
- Sandia National Laboratory, Livermore, CA, USA
| | - Jon K Magnuson
- Joint BioEnergy Institute, Emeryville, CA, USA.
- Pacific Northwest National Laboratory, Richland, WA, USA.
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30
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Geng T, Smallwood CR, Bredeweg EL, Pomraning KR, Plymale AE, Baker SE, Evans JE, Kelly RT. Multimodal microfluidic platform for controlled culture and analysis of unicellular organisms. Biomicrofluidics 2017; 11:054104. [PMID: 28966700 PMCID: PMC5608609 DOI: 10.1063/1.4986533] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 09/06/2017] [Indexed: 06/07/2023]
Abstract
Modern live-cell imaging approaches permit real-time visualization of biological processes, yet limitations exist for unicellular organism isolation, culturing, and long-term imaging that preclude fully understanding how cells sense and respond to environmental perturbations and the link between single-cell variability and whole-population dynamics. Here, we present a microfluidic platform that provides fine control over the local environment with the capacity to replace media components at any experimental time point, and provides both perfused and compartmentalized cultivation conditions depending on the valve configuration. The functionality and flexibility of the platform were validated using both bacteria and yeast having different sizes, motility, and growth media. The demonstrated ability to track the growth and dynamics of both motile and non-motile prokaryotic and eukaryotic organisms emphasizes the versatility of the devices, which should enable studies in bioenergy and environmental research.
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Affiliation(s)
- Tao Geng
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory Richland, Washington 99354, USA
| | - Chuck R Smallwood
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory Richland, Washington 99354, USA
| | - Erin L Bredeweg
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory Richland, Washington 99354, USA
| | - Kyle R Pomraning
- Energy Processes and Materials Division, Pacific Northwest National Laboratory Richland, Washington 99354, USA
| | - Andrew E Plymale
- Biological Sciences Division, Pacific Northwest National Laboratory Richland, Washington 99354, USA
| | - Scott E Baker
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory Richland, Washington 99354, USA
| | - James E Evans
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory Richland, Washington 99354, USA
| | - Ryan T Kelly
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory Richland, Washington 99354, USA
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31
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Abstract
Comprehensive and predictive simulation of coupled reaction networks has long been a goal of biology and other fields. Currently, metabolic network models that utilize enzyme mass action kinetics have predictive power but are limited in scope and application by the fact that the determination of enzyme rate constants is laborious and low throughput. We present a statistical thermodynamic formulation of the law of mass action for coupled reactions at both steady states and non-stationary states. The formulation uses chemical potentials instead of rate constants. When used to model deterministic systems, the method corresponds to a rescaling of the time dependent reactions in such a way that steady states can be reached on the same time scale but with significantly fewer computational steps. The relationships between reaction affinities, free energy changes and generalized detailed balance are central to the discussion. The significance for applications in systems biology are discussed as is the concept and assumption of maximum entropy production rate as a biological principle that links thermodynamics to natural selection.
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Affiliation(s)
- William R Cannon
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99352, United States of America. Author to whom any correspondence should be addressed
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32
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Haitjema CH, Gilmore SP, Henske JK, Solomon KV, de Groot R, Kuo A, Mondo SJ, Salamov AA, LaButti K, Zhao Z, Chiniquy J, Barry K, Brewer HM, Purvine SO, Wright AT, Hainaut M, Boxma B, van Alen T, Hackstein JHP, Henrissat B, Baker SE, Grigoriev IV, O'Malley MA. A parts list for fungal cellulosomes revealed by comparative genomics. Nat Microbiol 2017; 2:17087. [PMID: 28555641 DOI: 10.1038/nmicrobiol.2017.87] [Citation(s) in RCA: 126] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 04/25/2017] [Indexed: 12/16/2022]
Abstract
Cellulosomes are large, multiprotein complexes that tether plant biomass-degrading enzymes together for improved hydrolysis1. These complexes were first described in anaerobic bacteria, where species-specific dockerin domains mediate the assembly of enzymes onto cohesin motifs interspersed within protein scaffolds1. The versatile protein assembly mechanism conferred by the bacterial cohesin-dockerin interaction is now a standard design principle for synthetic biology2,3. For decades, analogous structures have been reported in anaerobic fungi, which are known to assemble by sequence-divergent non-catalytic dockerin domains (NCDDs)4. However, the components, modular assembly mechanism and functional role of fungal cellulosomes remain unknown5,6. Here, we describe a comprehensive set of proteins critical to fungal cellulosome assembly, including conserved scaffolding proteins unique to the Neocallimastigomycota. High-quality genomes of the anaerobic fungi Anaeromyces robustus, Neocallimastix californiae and Piromyces finnis were assembled with long-read, single-molecule technology. Genomic analysis coupled with proteomic validation revealed an average of 312 NCDD-containing proteins per fungal strain, which were overwhelmingly carbohydrate active enzymes (CAZymes), with 95 large fungal scaffoldins identified across four genera that bind to NCDDs. Fungal dockerin and scaffoldin domains have no similarity to their bacterial counterparts, yet several catalytic domains originated via horizontal gene transfer with gut bacteria. However, the biocatalytic activity of anaerobic fungal cellulosomes is expanded by the inclusion of GH3, GH6 and GH45 enzymes. These findings suggest that the fungal cellulosome is an evolutionarily chimaeric structure-an independently evolved fungal complex that co-opted useful activities from bacterial neighbours within the gut microbiome.
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Affiliation(s)
- Charles H Haitjema
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA
| | - Sean P Gilmore
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA
| | - John K Henske
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA
| | - Kevin V Solomon
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA
| | - Randall de Groot
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA
| | - Alan Kuo
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA
| | - Stephen J Mondo
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA
| | - Asaf A Salamov
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA
| | - Kurt LaButti
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA
| | - Zhiying Zhao
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA
| | - Jennifer Chiniquy
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA
| | - Heather M Brewer
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Samuel O Purvine
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Aaron T Wright
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Matthieu Hainaut
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique, Aix-Marseille Université, 13288 Marseille, France.,INRA, USC 1408 AFMB, Marseille, France
| | - Brigitte Boxma
- Department of Evolutionary Microbiology, Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - Theo van Alen
- Department of Evolutionary Microbiology, Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - Johannes H P Hackstein
- Department of Evolutionary Microbiology, Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique, Aix-Marseille Université, 13288 Marseille, France.,INRA, USC 1408 AFMB, Marseille, France.,Department of Biological Sciences, King Abdulaziz University, 23218 Jeddah, Saudi Arabia
| | - Scott E Baker
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA.,Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
| | - Michelle A O'Malley
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA
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33
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Schuerg T, Gabriel R, Baecker N, Baker SE, Singer SW. Thermoascus aurantiacus is an Intriguing Host for the Industrial Production of Cellulases. ACTA ACUST UNITED AC 2017. [DOI: 10.2174/2211550105666160520123504] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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34
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Bredeweg EL, Pomraning KR, Dai Z, Nielsen J, Kerkhoven EJ, Baker SE. Erratum to: A molecular genetic toolbox for Yarrowia lipolytica. Biotechnol Biofuels 2017; 10:45. [PMID: 28239417 PMCID: PMC5320769 DOI: 10.1186/s13068-017-0731-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 02/10/2017] [Indexed: 06/06/2023]
Abstract
[This corrects the article DOI: 10.1186/s13068-016-0687-7.].
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Affiliation(s)
- Erin L. Bredeweg
- Earth and Biological Sciences Directorate, Environmental Molecular Sciences Laboratory, Richland, WA 99354 USA
- Department of Energy, Battelle EMSL, 3335 Innovation Blvd, Richland, WA 99354 USA
| | - Kyle R. Pomraning
- Chemical & Biological Process Development Group, Energy and Environment Directorate, Pacific Northwest National Laboratories, Richland, WA 99354 USA
| | - Ziyu Dai
- Chemical & Biological Process Development Group, Energy and Environment Directorate, Pacific Northwest National Laboratories, Richland, WA 99354 USA
| | - Jens Nielsen
- Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
| | - Eduard J. Kerkhoven
- Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
| | - Scott E. Baker
- Earth and Biological Sciences Directorate, Environmental Molecular Sciences Laboratory, Richland, WA 99354 USA
- Department of Energy, Battelle EMSL, 3335 Innovation Blvd, Richland, WA 99354 USA
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35
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McCluskey K, Baker SE. Diverse data supports the transition of filamentous fungal model organisms into the post-genomics era. Mycology 2017; 8:67-83. [PMID: 30123633 PMCID: PMC6059044 DOI: 10.1080/21501203.2017.1281849] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 01/10/2017] [Indexed: 01/14/2023] Open
Abstract
Filamentous fungi have been important as model organisms since the beginning of modern biological inquiry and have benefitted from open data since the earliest genetic maps were shared. From early origins in simple Mendelian genetics of mating types, parasexual genetics of colony colour, and the foundational demonstration of the segregation of a nutritional requirement, the contribution of research systems utilising filamentous fungi has spanned the biochemical genetics era, through the molecular genetics era, and now are at the very foundation of diverse omics approaches to research and development. Fungal model organisms have come from most major taxonomic groups although Ascomycete filamentous fungi have seen the most major sustained effort. In addition to the published material about filamentous fungi, shared molecular tools have found application in every area of fungal biology. Similarly, shared data has contributed to the success of model systems. The scale of data supporting research with filamentous fungi has grown by 10 to 12 orders of magnitude. From genetic to molecular maps, expression databases, and finally genome resources, the open and collaborative nature of the research communities has assured that the rising tide of data has lifted all of the research systems together.
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Affiliation(s)
- Kevin McCluskey
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Scott E. Baker
- Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
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de Vries RP, Riley R, Wiebenga A, Aguilar-Osorio G, Amillis S, Uchima CA, Anderluh G, Asadollahi M, Askin M, Barry K, Battaglia E, Bayram Ö, Benocci T, Braus-Stromeyer SA, Caldana C, Cánovas D, Cerqueira GC, Chen F, Chen W, Choi C, Clum A, dos Santos RAC, Damásio ARDL, Diallinas G, Emri T, Fekete E, Flipphi M, Freyberg S, Gallo A, Gournas C, Habgood R, Hainaut M, Harispe ML, Henrissat B, Hildén KS, Hope R, Hossain A, Karabika E, Karaffa L, Karányi Z, Kraševec N, Kuo A, Kusch H, LaButti K, Lagendijk EL, Lapidus A, Levasseur A, Lindquist E, Lipzen A, Logrieco AF, MacCabe A, Mäkelä MR, Malavazi I, Melin P, Meyer V, Mielnichuk N, Miskei M, Molnár ÁP, Mulé G, Ngan CY, Orejas M, Orosz E, Ouedraogo JP, Overkamp KM, Park HS, Perrone G, Piumi F, Punt PJ, Ram AFJ, Ramón A, Rauscher S, Record E, Riaño-Pachón DM, Robert V, Röhrig J, Ruller R, Salamov A, Salih NS, Samson RA, Sándor E, Sanguinetti M, Schütze T, Sepčić K, Shelest E, Sherlock G, Sophianopoulou V, Squina FM, Sun H, Susca A, Todd RB, Tsang A, Unkles SE, van de Wiele N, van Rossen-Uffink D, Oliveira JVDC, Vesth TC, Visser J, Yu JH, Zhou M, Andersen MR, Archer DB, Baker SE, Benoit I, Brakhage AA, Braus GH, Fischer R, Frisvad JC, Goldman GH, Houbraken J, Oakley B, Pócsi I, Scazzocchio C, Seiboth B, vanKuyk PA, Wortman J, Dyer PS, Grigoriev IV. Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus. Genome Biol 2017; 18:28. [PMID: 28196534 PMCID: PMC5307856 DOI: 10.1186/s13059-017-1151-0] [Citation(s) in RCA: 311] [Impact Index Per Article: 44.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 01/10/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The fungal genus Aspergillus is of critical importance to humankind. Species include those with industrial applications, important pathogens of humans, animals and crops, a source of potent carcinogenic contaminants of food, and an important genetic model. The genome sequences of eight aspergilli have already been explored to investigate aspects of fungal biology, raising questions about evolution and specialization within this genus. RESULTS We have generated genome sequences for ten novel, highly diverse Aspergillus species and compared these in detail to sister and more distant genera. Comparative studies of key aspects of fungal biology, including primary and secondary metabolism, stress response, biomass degradation, and signal transduction, revealed both conservation and diversity among the species. Observed genomic differences were validated with experimental studies. This revealed several highlights, such as the potential for sex in asexual species, organic acid production genes being a key feature of black aspergilli, alternative approaches for degrading plant biomass, and indications for the genetic basis of stress response. A genome-wide phylogenetic analysis demonstrated in detail the relationship of the newly genome sequenced species with other aspergilli. CONCLUSIONS Many aspects of biological differences between fungal species cannot be explained by current knowledge obtained from genome sequences. The comparative genomics and experimental study, presented here, allows for the first time a genus-wide view of the biological diversity of the aspergilli and in many, but not all, cases linked genome differences to phenotype. Insights gained could be exploited for biotechnological and medical applications of fungi.
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Affiliation(s)
- Ronald P. de Vries
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Robert Riley
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Ad Wiebenga
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Guillermo Aguilar-Osorio
- Department of Food Science and Biotechnology, Faculty of Chemistry, National University of Mexico, Ciudad Universitaria, D.F. C.P. 04510 Mexico
| | - Sotiris Amillis
- Department of Biology, National and Kapodistrian University of Athens, Panepistimioupolis, 15781 Athens, Greece
| | - Cristiane Akemi Uchima
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192 CEP 13083-970, Campinas, São Paulo Brasil
- Present address: VTT Brasil, Alameda Inajá, 123, CEP 06460-055 Barueri, São Paulo Brazil
| | - Gregor Anderluh
- Laboratory for Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Mojtaba Asadollahi
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, 4032 Debrecen, Hungary
| | - Marion Askin
- Institute of Biology Leiden, Molecular Microbiology and Biotechnology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
- Present address: CSIRO Publishing, Unipark, Building 1 Level 1, 195 Wellington Road, Clayton, VIC 3168 Australia
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Evy Battaglia
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Özgür Bayram
- Department of Molecular Microbiology and Genetics, Institute for Microbiology and Genetics, Georg August University Göttingen, Grisebachstr. 8, 37077 Göttingen, Germany
- Department of Biology, Maynooth University, Maynooth, Co. Kildare Ireland
| | - Tiziano Benocci
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Susanna A. Braus-Stromeyer
- Department of Molecular Microbiology and Genetics, Institute for Microbiology and Genetics, Georg August University Göttingen, Grisebachstr. 8, 37077 Göttingen, Germany
| | - Camila Caldana
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192 CEP 13083-970, Campinas, São Paulo Brasil
- Max Planck Partner Group, Brazilian Bioethanol Science and Technology Laboratory, CEP 13083-100 Campinas, Sao Paulo Brazil
| | - David Cánovas
- Department of Genetics, Faculty of Biology, University of Seville, Avda de Reina Mercedes 6, 41012 Sevilla, Spain
- Fungal Genetics and Genomics Unit, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences (BOKU) Vienna, Vienna, Austria
| | | | - Fusheng Chen
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Wanping Chen
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Cindy Choi
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Alicia Clum
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Renato Augusto Corrêa dos Santos
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192 CEP 13083-970, Campinas, São Paulo Brasil
| | - André Ricardo de Lima Damásio
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192 CEP 13083-970, Campinas, São Paulo Brasil
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, CEP 13083-862 Campinas, SP Brazil
| | - George Diallinas
- Department of Biology, National and Kapodistrian University of Athens, Panepistimioupolis, 15781 Athens, Greece
| | - Tamás Emri
- Department of Biotechnology and Microbiology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
| | - Erzsébet Fekete
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, 4032 Debrecen, Hungary
| | - Michel Flipphi
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, 4032 Debrecen, Hungary
| | - Susanne Freyberg
- Department of Molecular Microbiology and Genetics, Institute for Microbiology and Genetics, Georg August University Göttingen, Grisebachstr. 8, 37077 Göttingen, Germany
| | - Antonia Gallo
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), via Provinciale Lecce-Monteroni, 73100 Lecce, Italy
| | - Christos Gournas
- Institute of Biosciences and Applications, Microbial Molecular Genetics Laboratory, National Center for Scientific Research, Demokritos (NCSRD), Athens, Greece
- Present address: Université Libre de Bruxelles Institute of Molecular Biology and Medicine (IBMM), Brussels, Belgium
| | - Rob Habgood
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
| | | | - María Laura Harispe
- Institut Pasteur de Montevideo, Unidad Mixta INIA-IPMont, Mataojo 2020, CP11400 Montevideo, Uruguay
- Present address: Instituto de Profesores Artigas, Consejo de Formación en Educación, ANEP, CP 11800, Av. del Libertador 2025, Montevideo, Uruguay
| | - Bernard Henrissat
- CNRS, Aix-Marseille Université, Marseille, France
- INRA, USC 1408 AFMB, 13288 Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Kristiina S. Hildén
- Department of Food and Environmental Sciences, University of Helsinki, Viikinkaari 9, Helsinki, Finland
| | - Ryan Hope
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
| | - Abeer Hossain
- Dutch DNA Biotech BV, Utrechtseweg 48, 3703AJ Zeist, The Netherlands
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Eugenia Karabika
- School of Biology, University of St Andrews, St Andrews, Fife KY16 9TH UK
- Present Address: Department of Chemistry, University of Ioannina, Ioannina, 45110 Greece
| | - Levente Karaffa
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, 4032 Debrecen, Hungary
| | - Zsolt Karányi
- Department of Medicine, Faculty of Medicine, University of Debrecen, Nagyerdei krt. 98, 4032 Debrecen, Hungary
| | - Nada Kraševec
- Laboratory for Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Alan Kuo
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Harald Kusch
- Department of Molecular Microbiology and Genetics, Institute for Microbiology and Genetics, Georg August University Göttingen, Grisebachstr. 8, 37077 Göttingen, Germany
- Department of Medical Informatics, University Medical Centre, Robert-Koch-Str.40, 37075 Göttingen, Germany
- Department of Molecular Biology, Universitätsmedizin Göttingen, Humboldtallee 23, Göttingen, 37073 Germany
| | - Kurt LaButti
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Ellen L. Lagendijk
- Institute of Biology Leiden, Molecular Microbiology and Biotechnology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Alla Lapidus
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
- Present address: Center for Algorithmic Biotechnology, St.Petersburg State University, St. Petersburg, Russia
| | - Anthony Levasseur
- INRA, Aix-Marseille Univ, BBF, Biodiversité et Biotechnologie Fongiques, Marseille, France
- Present address: Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63, CNRS 7278, IRD 198, INSERM U1095, IHU Méditerranée Infection, Pôle des Maladies Infectieuses, Assistance Publique-Hôpitaux de Marseille, Faculté de Médecine, 27 Bd Jean Moulin, 13005 Marseille, France
| | - Erika Lindquist
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Antonio F. Logrieco
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Via Amendola 122/O, 70126 Bari, Italy
| | - Andrew MacCabe
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos, Consejo Superior de Investigaciones Científicas (CSIC), Paterna, Valencia, Spain
| | - Miia R. Mäkelä
- Department of Food and Environmental Sciences, University of Helsinki, Viikinkaari 9, Helsinki, Finland
| | - Iran Malavazi
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Carlos, São Paulo Brazil
| | - Petter Melin
- Uppsala BioCenter, Department of Microbiology, Swedish University of Agricultural Sciences, P.O. Box 7025, 750 07 Uppsala, Sweden
- Present address: Swedish Chemicals Agency, Box 2, 172 13 Sundbyberg, Sweden
| | - Vera Meyer
- Institute of Biotechnology, Department Applied and Molecular Microbiology, Berlin University of Technology, Gustav-Meyer-Allee 25, 13355 Berlin, Germany
| | - Natalia Mielnichuk
- Department of Genetics, Faculty of Biology, University of Seville, Avda de Reina Mercedes 6, 41012 Sevilla, Spain
- Present address: Instituto de Ciencia y Tecnología Dr. César Milstein, Fundación Pablo Cassará, CONICET, Saladillo 2468 C1440FFX, Ciudad de Buenos Aires, Argentina
| | - Márton Miskei
- Department of Biotechnology and Microbiology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
- MTA-DE Momentum, Laboratory of Protein Dynamics, Department of Biochemistry and Molecular Biology, University of Debrecen, Nagyerdei krt.98., 4032 Debrecen, Hungary
| | - Ákos P. Molnár
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, 4032 Debrecen, Hungary
| | - Giuseppina Mulé
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Via Amendola 122/O, 70126 Bari, Italy
| | - Chew Yee Ngan
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Margarita Orejas
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos, Consejo Superior de Investigaciones Científicas (CSIC), Paterna, Valencia, Spain
| | - Erzsébet Orosz
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Department of Biotechnology and Microbiology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
| | - Jean Paul Ouedraogo
- Institute of Biology Leiden, Molecular Microbiology and Biotechnology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
- Present address: Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montreal, QC H4B 1R6 Canada
| | - Karin M. Overkamp
- Dutch DNA Biotech BV, Utrechtseweg 48, 3703AJ Zeist, The Netherlands
| | - Hee-Soo Park
- School of Food Science and Biotechnology, Kyungpook National University, Daegu, 702-701 Republic of Korea
| | - Giancarlo Perrone
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Via Amendola 122/O, 70126 Bari, Italy
| | - Francois Piumi
- INRA, Aix-Marseille Univ, BBF, Biodiversité et Biotechnologie Fongiques, Marseille, France
- Present address: INRA UMR1198 Biologie du Développement et de la Reproduction - Domaine de Vilvert, Jouy en Josas, 78352 Cedex France
| | - Peter J. Punt
- Institute of Biology Leiden, Molecular Microbiology and Biotechnology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
- Dutch DNA Biotech BV, Utrechtseweg 48, 3703AJ Zeist, The Netherlands
| | - Arthur F. J. Ram
- Institute of Biology Leiden, Molecular Microbiology and Biotechnology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Ana Ramón
- Sección Bioquímica, Departamento de Biología Celular y Molecular, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Stefan Rauscher
- Department of Microbiology, Karlsruhe Institute of Technology, Institute for Applied Biosciences, Hertzstrasse 16,, 76187 Karlsruhe, Germany
| | - Eric Record
- INRA, Aix-Marseille Univ, BBF, Biodiversité et Biotechnologie Fongiques, Marseille, France
| | - Diego Mauricio Riaño-Pachón
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192 CEP 13083-970, Campinas, São Paulo Brasil
| | - Vincent Robert
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Julian Röhrig
- Department of Microbiology, Karlsruhe Institute of Technology, Institute for Applied Biosciences, Hertzstrasse 16,, 76187 Karlsruhe, Germany
| | - Roberto Ruller
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192 CEP 13083-970, Campinas, São Paulo Brasil
| | - Asaf Salamov
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Nadhira S. Salih
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
- Department of Biology, School of Science, University of Sulaimani, Al Sulaymaneyah, Iraq
| | - Rob A. Samson
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Erzsébet Sándor
- Institute of Food Science, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, 4032 Debrecen, Hungary
| | - Manuel Sanguinetti
- Sección Bioquímica, Departamento de Biología Celular y Molecular, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Tabea Schütze
- Institute of Biology Leiden, Molecular Microbiology and Biotechnology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
- Present address: Department Applied and Molecular Microbiology, Institute of Biotechnology, Berlin University of Technology, Gustav-Meyer-Allee 25, 13355 Berlin, Germany
| | - Kristina Sepčić
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia
| | - Ekaterina Shelest
- Systems Biology/Bioinformatics group, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute, (HKI), Beutenbergstr. 11a, 07745 Jena, Germany
| | - Gavin Sherlock
- Department of Genetics, Stanford University, Stanford, CA 94305-5120 USA
| | - Vicky Sophianopoulou
- Institute of Biosciences and Applications, Microbial Molecular Genetics Laboratory, National Center for Scientific Research, Demokritos (NCSRD), Athens, Greece
| | - Fabio M. Squina
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192 CEP 13083-970, Campinas, São Paulo Brasil
| | - Hui Sun
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Antonia Susca
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Via Amendola 122/O, 70126 Bari, Italy
| | - Richard B. Todd
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506 USA
| | - Adrian Tsang
- Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montreal, QC H4B 1R6 Canada
| | - Shiela E. Unkles
- School of Biology, University of St Andrews, St Andrews, Fife KY16 9TH UK
| | - Nathalie van de Wiele
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Diana van Rossen-Uffink
- Institute of Biology Leiden, Molecular Microbiology and Biotechnology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
- Present address: BaseClear B.V., Einsteinweg 5, 2333 CC Leiden, The Netherlands
| | - Juliana Velasco de Castro Oliveira
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192 CEP 13083-970, Campinas, São Paulo Brasil
| | - Tammi C. Vesth
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 223, 2800 Kongens Lyngby, Denmark
| | - Jaap Visser
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Jae-Hyuk Yu
- Departments of Bacteriology and Genetics, University of Wisconsin-Madison, 1550 Linden Drive, Madison, WI 53706 USA
| | - Miaomiao Zhou
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Mikael R. Andersen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 223, 2800 Kongens Lyngby, Denmark
| | - David B. Archer
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
| | - Scott E. Baker
- Fungal Biotechnology Team, Pacific Northwest National Laboratory, Richland, Washington, 99352 USA
| | - Isabelle Benoit
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Present address: Centre of Functional and Structure Genomics Biology Department Concordia University, 7141 Sherbrooke St. W., Montreal, QC H4B 1R6 Canada
| | - Axel A. Brakhage
- Department of Molecular and Applied Microbiology, Leibniz-Institute for Natural Product Research and Infection Biology - Hans Knoell Institute (HKI) and Institute for Microbiology, Friedrich Schiller University Jena, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Gerhard H. Braus
- Department of Molecular Microbiology and Genetics, Institute for Microbiology and Genetics, Georg August University Göttingen, Grisebachstr. 8, 37077 Göttingen, Germany
| | - Reinhard Fischer
- Department of Microbiology, Karlsruhe Institute of Technology, Institute for Applied Biosciences, Hertzstrasse 16,, 76187 Karlsruhe, Germany
| | - Jens C. Frisvad
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 223, 2800 Kongens Lyngby, Denmark
| | - Gustavo H. Goldman
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. do Café S/N, CEP 14040-903 Ribeirão Preto, São Paulo Brazil
| | - Jos Houbraken
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Berl Oakley
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045 USA
| | - István Pócsi
- Department of Biotechnology and Microbiology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
| | - Claudio Scazzocchio
- Department of Microbiology, Imperial College, London, SW7 2AZ UK
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris‐Sud, Université Paris‐Saclay, 91198 Gif‐sur‐Yvette cedex, France
| | - Bernhard Seiboth
- Research Division Biochemical Technology, Institute of Chemical Engineering, TU Wien, Gumpendorferstraße 1a, 1060 Vienna, Austria
| | - Patricia A. vanKuyk
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Institute of Biology Leiden, Molecular Microbiology and Biotechnology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Jennifer Wortman
- Broad Institute, 415 Main St, Cambridge, MA 02142 USA
- Present address: Seres Therapeutics, 200 Sidney St, Cambridge, MA 02139 USA
| | - Paul S. Dyer
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
| | - Igor V. Grigoriev
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
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Bredeweg EL, Pomraning KR, Dai Z, Nielsen J, Kerkhoven EJ, Baker SE. A molecular genetic toolbox for Yarrowia lipolytica. Biotechnol Biofuels 2017; 10:2. [PMID: 28066508 PMCID: PMC5210315 DOI: 10.1186/s13068-016-0687-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 12/13/2016] [Indexed: 05/29/2023]
Abstract
BACKGROUND Yarrowia lipolytica is an ascomycete yeast used in biotechnological research for its abilities to secrete high concentrations of proteins and accumulate lipids. Genetic tools have been made in a variety of backgrounds with varying similarity to a comprehensively sequenced strain. RESULTS We have developed a set of genetic and molecular tools in order to expand capabilities of Y. lipolytica for both biological research and industrial bioengineering applications. In this work, we generated a set of isogenic auxotrophic strains with decreased non-homologous end joining for targeted DNA incorporation. Genome sequencing, assembly, and annotation of this genetic background uncovers previously unidentified genes in Y. lipolytica. To complement these strains, we constructed plasmids with Y. lipolytica-optimized superfolder GFP for targeted overexpression and fluorescent tagging. We used these tools to build the "Yarrowia lipolytica Cell Atlas," a collection of strains with endogenous fluorescently tagged organelles in the same genetic background, in order to define organelle morphology in live cells. CONCLUSIONS These molecular and isogenetic tools are useful for live assessment of organelle-specific protein expression, and for localization of lipid biosynthetic enzymes or other proteins in Y. lipolytica. This work provides the Yarrowia community with tools for cell biology and metabolism research in Y. lipolytica for further development of biofuels and natural products.
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Affiliation(s)
- Erin L. Bredeweg
- Earth and Biological Sciences Directorate, Environmental Molecular Sciences Laboratory, Richland, WA 99354 USA
- Department of Energy, Battelle EMSL, 3335 Innovation Blvd, Richland, WA 99354 USA
| | - Kyle R. Pomraning
- Chemical & Biological Process Development Group, Energy and Environment Directorate, Pacific Northwest National Laboratories, Richland, WA 99354 USA
| | - Ziyu Dai
- Chemical & Biological Process Development Group, Energy and Environment Directorate, Pacific Northwest National Laboratories, Richland, WA 99354 USA
| | - Jens Nielsen
- Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
| | - Eduard J. Kerkhoven
- Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
| | - Scott E. Baker
- Earth and Biological Sciences Directorate, Environmental Molecular Sciences Laboratory, Richland, WA 99354 USA
- Department of Energy, Battelle EMSL, 3335 Innovation Blvd, Richland, WA 99354 USA
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Ivanova C, Ramoni J, Aouam T, Frischmann A, Seiboth B, Baker SE, Le Crom S, Lemoine S, Margeot A, Bidard F. Genome sequencing and transcriptome analysis of Trichoderma reesei QM9978 strain reveals a distal chromosome translocation to be responsible for loss of vib1 expression and loss of cellulase induction. Biotechnol Biofuels 2017; 10:209. [PMID: 28912831 PMCID: PMC5588705 DOI: 10.1186/s13068-017-0897-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 08/29/2017] [Indexed: 05/05/2023]
Abstract
BACKGROUND The hydrolysis of biomass to simple sugars used for the production of biofuels in biorefineries requires the action of cellulolytic enzyme mixtures. During the last 50 years, the ascomycete Trichoderma reesei, the main source of industrial cellulase and hemicellulase cocktails, has been subjected to several rounds of classical mutagenesis with the aim to obtain higher production levels. During these random genetic events, strains unable to produce cellulases were generated. Here, whole genome sequencing and transcriptomic analyses of the cellulase-negative strain QM9978 were used for the identification of mutations underlying this cellulase-negative phenotype. RESULTS Sequence comparison of the cellulase-negative strain QM9978 to the reference strain QM6a identified a total of 43 mutations, of which 33 were located either close to or in coding regions. From those, we identified 23 single-nucleotide variants, nine InDels, and one translocation. The translocation occurred between chromosomes V and VII, is located upstream of the putative transcription factor vib1, and abolishes its expression in QM9978 as detected during the transcriptomic analyses. Ectopic expression of vib1 under the control of its native promoter as well as overexpression of vib1 under the control of a strong constitutive promoter restored cellulase expression in QM9978, thus confirming that the translocation event is the reason for the cellulase-negative phenotype. Gene deletion of vib1 in the moderate producer strain QM9414 and in the high producer strain Rut-C30 reduced cellulase expression in both cases. Overexpression of vib1 in QM9414 and Rut-C30 had no effect on cellulase production, most likely because vib1 is already expressed at an optimal level under normal conditions. CONCLUSION We were able to establish a link between a chromosomal translocation in QM9978 and the cellulase-negative phenotype of the strain. We identified the transcription factor vib1 as a key regulator of cellulases in T. reesei whose expression is absent in QM9978. We propose that in T. reesei, as in Neurospora crassa, vib1 is involved in cellulase induction, although the exact mechanism remains to be elucidated. The data presented here show an example of a combined genome sequencing and transcriptomic approach to explain a specific trait, in this case the QM9978 cellulase-negative phenotype, and how it helps to better understand the mechanisms during cellulase gene regulation. When focusing on mutations on the single base-pair level, changes on the chromosome level can be easily overlooked and through this work we provide an example that stresses the importance of the big picture of the genomic landscape during analysis of sequencing data.
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Affiliation(s)
- Christa Ivanova
- IFP Energies Nouvelles, 1-4 Avenue de Bois-Préau, 92852 Rueil-Malmaison, France
- Present Address: Genetics of Biofilms Unit, Department of Microbiology, Institut Pasteur, 25-28 Rue du Dr Roux, 75015 Paris, France
| | - Jonas Ramoni
- Molecular Biotechnology, Research Division Biochemical Technology, Institute of Chemical Engineering, TU-Wien, 1060 Vienna, Austria
| | - Thiziri Aouam
- IFP Energies Nouvelles, 1-4 Avenue de Bois-Préau, 92852 Rueil-Malmaison, France
| | - Alexa Frischmann
- Molecular Biotechnology, Research Division Biochemical Technology, Institute of Chemical Engineering, TU-Wien, 1060 Vienna, Austria
| | - Bernhard Seiboth
- Molecular Biotechnology, Research Division Biochemical Technology, Institute of Chemical Engineering, TU-Wien, 1060 Vienna, Austria
| | - Scott E. Baker
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99354 USA
| | - Stéphane Le Crom
- Evolution Paris Seine-Institut de Biologie Paris Seine (EPS-IBPS), Sorbonne Universités, UPMC Univ Paris 06, Univ Antilles, Univ Nice Sophia Antipolis, CNRS, 75005 Paris, France
| | - Sophie Lemoine
- École normale supérieure, PSL Research University, CNRS, Inserm, Institut de Biologie de l’École normale supérieure (IBENS), Plateforme Génomique, 75005 Paris, France
| | - Antoine Margeot
- IFP Energies Nouvelles, 1-4 Avenue de Bois-Préau, 92852 Rueil-Malmaison, France
| | - Frédérique Bidard
- IFP Energies Nouvelles, 1-4 Avenue de Bois-Préau, 92852 Rueil-Malmaison, France
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Corrochano LM, Kuo A, Marcet-Houben M, Polaino S, Salamov A, Villalobos-Escobedo JM, Grimwood J, Álvarez MI, Avalos J, Bauer D, Benito EP, Benoit I, Burger G, Camino LP, Cánovas D, Cerdá-Olmedo E, Cheng JF, Domínguez A, Eliáš M, Eslava AP, Glaser F, Gutiérrez G, Heitman J, Henrissat B, Iturriaga EA, Lang BF, Lavín JL, Lee SC, Li W, Lindquist E, López-García S, Luque EM, Marcos AT, Martin J, McCluskey K, Medina HR, Miralles-Durán A, Miyazaki A, Muñoz-Torres E, Oguiza JA, Ohm RA, Olmedo M, Orejas M, Ortiz-Castellanos L, Pisabarro AG, Rodríguez-Romero J, Ruiz-Herrera J, Ruiz-Vázquez R, Sanz C, Schackwitz W, Shahriari M, Shelest E, Silva-Franco F, Soanes D, Syed K, Tagua VG, Talbot NJ, Thon MR, Tice H, de Vries RP, Wiebenga A, Yadav JS, Braun EL, Baker SE, Garre V, Schmutz J, Horwitz BA, Torres-Martínez S, Idnurm A, Herrera-Estrella A, Gabaldón T, Grigoriev IV. Expansion of Signal Transduction Pathways in Fungi by Extensive Genome Duplication. Curr Biol 2016; 26:1577-1584. [PMID: 27238284 DOI: 10.1016/j.cub.2016.04.038] [Citation(s) in RCA: 131] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 03/22/2016] [Accepted: 04/13/2016] [Indexed: 02/03/2023]
Abstract
Plants and fungi use light and other signals to regulate development, growth, and metabolism. The fruiting bodies of the fungus Phycomyces blakesleeanus are single cells that react to environmental cues, including light, but the mechanisms are largely unknown [1]. The related fungus Mucor circinelloides is an opportunistic human pathogen that changes its mode of growth upon receipt of signals from the environment to facilitate pathogenesis [2]. Understanding how these organisms respond to environmental cues should provide insights into the mechanisms of sensory perception and signal transduction by a single eukaryotic cell, and their role in pathogenesis. We sequenced the genomes of P. blakesleeanus and M. circinelloides and show that they have been shaped by an extensive genome duplication or, most likely, a whole-genome duplication (WGD), which is rarely observed in fungi [3-6]. We show that the genome duplication has expanded gene families, including those involved in signal transduction, and that duplicated genes have specialized, as evidenced by differences in their regulation by light. The transcriptional response to light varies with the developmental stage and is still observed in a photoreceptor mutant of P. blakesleeanus. A phototropic mutant of P. blakesleeanus with a heterozygous mutation in the photoreceptor gene madA demonstrates that photosensor dosage is important for the magnitude of signal transduction. We conclude that the genome duplication provided the means to improve signal transduction for enhanced perception of environmental signals. Our results will help to understand the role of genome dynamics in the evolution of sensory perception in eukaryotes.
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Affiliation(s)
- Luis M Corrochano
- Department of Genetics, University of Seville, Avenida Reina Mercedes s/n, 41012 Seville, Spain.
| | - Alan Kuo
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Marina Marcet-Houben
- Centre for Genomic Regulation (CRG), Doctor Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Doctor Aiguader 88, 08003 Barcelona, Spain
| | - Silvia Polaino
- School of Biological Sciences, University of Missouri-Kansas City, 5007 Rockhill Road, Kansas City, MO 64110, USA
| | - Asaf Salamov
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - José M Villalobos-Escobedo
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y Estudios Avanzados, Kilómetro 9.6 Libramiento Norte, Carretera Irapuato-León, 36821 Irapuato, Guanajuato, México
| | - Jane Grimwood
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA; HudsonAlpha Institute of Biotechnology, 601 Genome Way Northwest, Huntsville, AL 35806, USA
| | - M Isabel Álvarez
- Departamento de Microbiología y Genética, Universidad de Salamanca, Plaza de los doctores de la Reina s/n, 37007 Salamanca, Spain
| | - Javier Avalos
- Department of Genetics, University of Seville, Avenida Reina Mercedes s/n, 41012 Seville, Spain
| | - Diane Bauer
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Ernesto P Benito
- Departamento de Microbiología y Genética, Universidad de Salamanca, Plaza de los doctores de la Reina s/n, 37007 Salamanca, Spain; Instituto Hispano-Luso de Investigaciones Agrarias (CIALE), Universidad de Salamanca, Río Duero 12, 37185 Salamanca, Spain
| | - Isabelle Benoit
- CBS-KNAW Fungal Biodiversity Centre and Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Gertraud Burger
- Universite de Montreal, Pavillon Roger-Gaudry, Biochimie, CP 6128, Succursale Centre-Ville, Montreal QC, H3C 3J7, Canada
| | - Lola P Camino
- Department of Genetics, University of Seville, Avenida Reina Mercedes s/n, 41012 Seville, Spain
| | - David Cánovas
- Department of Genetics, University of Seville, Avenida Reina Mercedes s/n, 41012 Seville, Spain
| | - Enrique Cerdá-Olmedo
- Department of Genetics, University of Seville, Avenida Reina Mercedes s/n, 41012 Seville, Spain
| | - Jan-Fang Cheng
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Angel Domínguez
- Departamento de Microbiología y Genética, Universidad de Salamanca, Plaza de los doctores de la Reina s/n, 37007 Salamanca, Spain
| | - Marek Eliáš
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Chittussiho 10, 710 00 Ostrava, Czech Republic
| | - Arturo P Eslava
- Departamento de Microbiología y Genética, Universidad de Salamanca, Plaza de los doctores de la Reina s/n, 37007 Salamanca, Spain
| | - Fabian Glaser
- Lokey Interdisciplinary Center for Life Sciences and Engineering, Technion - Israel Institute of Technology, Haifa 3200003, Israel
| | - Gabriel Gutiérrez
- Department of Genetics, University of Seville, Avenida Reina Mercedes s/n, 41012 Seville, Spain
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Research Drive, Durham, NC 27710, USA
| | - Bernard Henrissat
- Centre National de la Recherche Scientifique (CNRS), UMR7257, Université Aix-Marseille, 163 Avenue de Luminy, 13288 Marseille, France; Department of Biological Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
| | - Enrique A Iturriaga
- Departamento de Microbiología y Genética, Universidad de Salamanca, Plaza de los doctores de la Reina s/n, 37007 Salamanca, Spain
| | - B Franz Lang
- Universite de Montreal, Pavillon Roger-Gaudry, Biochimie, CP 6128, Succursale Centre-Ville, Montreal QC, H3C 3J7, Canada
| | - José L Lavín
- Genome Analysis Platform, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Bizkaia, Spain
| | - Soo Chan Lee
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Research Drive, Durham, NC 27710, USA
| | - Wenjun Li
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Research Drive, Durham, NC 27710, USA
| | - Erika Lindquist
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Sergio López-García
- Departamento de Genética y Microbiología, Universidad de Murcia, 30071 Murcia, Spain
| | - Eva M Luque
- Department of Genetics, University of Seville, Avenida Reina Mercedes s/n, 41012 Seville, Spain
| | - Ana T Marcos
- Department of Genetics, University of Seville, Avenida Reina Mercedes s/n, 41012 Seville, Spain
| | - Joel Martin
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Kevin McCluskey
- Department of Plant Pathology, Kansas State University, 4024 Throckmorton Plant Sciences Center, Manhattan, KS 66506, USA
| | - Humberto R Medina
- Department of Genetics, University of Seville, Avenida Reina Mercedes s/n, 41012 Seville, Spain
| | | | - Atsushi Miyazaki
- Department of Biological Sciences, Faculty of Science and Engineering, Ishinomaki Senshu University, Ishinomaki 986-8580, Japan
| | - Elisa Muñoz-Torres
- Departamento de Biología Celular y Patología, Facultad de Medicina, Universidad de Salamanca, Avenida Campus Miguel de Unamuno, 37007 Salamanca, Spain
| | - José A Oguiza
- Department of Agrarian Production, Public University of Navarre, 31006 Pamplona, Spain
| | - Robin A Ohm
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - María Olmedo
- Department of Genetics, University of Seville, Avenida Reina Mercedes s/n, 41012 Seville, Spain
| | - Margarita Orejas
- Instituto de Agroquímica y Tecnología de Alimentos, Consejo Superior de Investigaciones Científicas (IATA-CSIC), Avenida Catedrático Agustín Escardino 7, 46980 Paterna, Valencia, Spain
| | - Lucila Ortiz-Castellanos
- Departamento de Ingeniería Genética, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Kilómetro 9.6 Libramiento Norte, Carretera Irapuato-León, 36821 Irapuato, Guanajuato, Mexico
| | - Antonio G Pisabarro
- Department of Agrarian Production, Public University of Navarre, 31006 Pamplona, Spain
| | - Julio Rodríguez-Romero
- Department of Genetics, University of Seville, Avenida Reina Mercedes s/n, 41012 Seville, Spain
| | - José Ruiz-Herrera
- Departamento de Ingeniería Genética, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Kilómetro 9.6 Libramiento Norte, Carretera Irapuato-León, 36821 Irapuato, Guanajuato, Mexico
| | - Rosa Ruiz-Vázquez
- Departamento de Genética y Microbiología, Universidad de Murcia, 30071 Murcia, Spain
| | - Catalina Sanz
- Departamento de Microbiología y Genética, Universidad de Salamanca, Plaza de los doctores de la Reina s/n, 37007 Salamanca, Spain
| | - Wendy Schackwitz
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Mahdi Shahriari
- Departamento de Microbiología y Genética, Universidad de Salamanca, Plaza de los doctores de la Reina s/n, 37007 Salamanca, Spain
| | - Ekaterina Shelest
- Leibniz Institute for Natural Product Research and Infection Biology (Hans Knoell Institute), Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Fátima Silva-Franco
- Departamento de Genética y Microbiología, Universidad de Murcia, 30071 Murcia, Spain
| | - Darren Soanes
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| | - Khajamohiddin Syed
- Department of Environmental Health, University of Cincinnati College of Medicine, 160 Panzeca Way, Cincinnati, OH 45267-0056, USA
| | - Víctor G Tagua
- Department of Genetics, University of Seville, Avenida Reina Mercedes s/n, 41012 Seville, Spain
| | - Nicholas J Talbot
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| | - Michael R Thon
- Departamento de Microbiología y Genética, Universidad de Salamanca, Plaza de los doctores de la Reina s/n, 37007 Salamanca, Spain; Instituto Hispano-Luso de Investigaciones Agrarias (CIALE), Universidad de Salamanca, Río Duero 12, 37185 Salamanca, Spain
| | - Hope Tice
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Ronald P de Vries
- CBS-KNAW Fungal Biodiversity Centre and Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Ad Wiebenga
- CBS-KNAW Fungal Biodiversity Centre and Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Jagjit S Yadav
- Department of Environmental Health, University of Cincinnati College of Medicine, 160 Panzeca Way, Cincinnati, OH 45267-0056, USA
| | - Edward L Braun
- Department of Biology, University of Florida, P.O. Box 118525, Gainesville, FL 32611-8525, USA
| | - Scott E Baker
- Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA 99352, USA
| | - Victoriano Garre
- Departamento de Genética y Microbiología, Universidad de Murcia, 30071 Murcia, Spain
| | - Jeremy Schmutz
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA; HudsonAlpha Institute of Biotechnology, 601 Genome Way Northwest, Huntsville, AL 35806, USA
| | - Benjamin A Horwitz
- Department of Biology, Technion - Israel Institute of Technology, Haifa 32000, Israel
| | | | - Alexander Idnurm
- School of Biological Sciences, University of Missouri-Kansas City, 5007 Rockhill Road, Kansas City, MO 64110, USA; School of BioSciences, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y Estudios Avanzados, Kilómetro 9.6 Libramiento Norte, Carretera Irapuato-León, 36821 Irapuato, Guanajuato, México
| | - Toni Gabaldón
- Centre for Genomic Regulation (CRG), Doctor Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Doctor Aiguader 88, 08003 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
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Goodwin SB, McCorison CB, Cavaletto JR, Culley DE, LaButti K, Baker SE, Grigoriev IV. The mitochondrial genome of the ethanol-metabolizing, wine cellar mold Zasmidium cellare is the smallest for a filamentous ascomycete. Fungal Biol 2016; 120:961-974. [PMID: 27521628 DOI: 10.1016/j.funbio.2016.05.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 03/31/2016] [Accepted: 05/07/2016] [Indexed: 01/26/2023]
Abstract
Fungi in the class Dothideomycetes often live in extreme environments or have unusual physiology. One of these, the wine cellar mold Zasmidium cellare, produces thick curtains of mycelia in cellars with high humidity, and its ability to metabolize volatile organic compounds is thought to improve air quality. Whether these abilities have affected its mitochondrial genome is not known. To fill this gap, the circular-mapping mitochondrial genome of Z. cellare was sequenced and, at only 23 743 bp, is the smallest reported for a filamentous fungus. Genes were encoded on both strands with a single change of direction, different from most other fungi but consistent with the Dothideomycetes. Other than its small size, the only unusual feature of the Z. cellare mitochondrial genome was two copies of a 110-bp sequence that were duplicated, inverted and separated by approximately 1 kb. This inverted-repeat sequence confused the assembly program but appears to have no functional significance. The small size of the Z. cellare mitochondrial genome was due to slightly smaller genes, lack of introns and non-essential genes, reduced intergenic spacers and very few ORFs relative to other fungi rather than a loss of essential genes. Whether this reduction facilitates its unusual biology remains unknown.
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Affiliation(s)
- Stephen B Goodwin
- USDA, Agricultural Research Service, Crop Production and Pest Control Research Unit, 915 West State Street, Purdue University, West Lafayette, IN 47907-2054, USA.
| | - Cassandra B McCorison
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907-2054, USA
| | - Jessica R Cavaletto
- USDA, Agricultural Research Service, Crop Production and Pest Control Research Unit, 915 West State Street, Purdue University, West Lafayette, IN 47907-2054, USA
| | - David E Culley
- Chemical and Biological Process Development Group, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, MSIN P8-60, Richland, WA 99352, USA
| | - Kurt LaButti
- U.S. Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Scott E Baker
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Blvd, Richland, WA 99354, USA
| | - Igor V Grigoriev
- U.S. Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
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Nguyen HDT, McMullin DR, Ponomareva E, Riley R, Pomraning KR, Baker SE, Seifert KA. Ochratoxin A production by Penicillium thymicola. Fungal Biol 2016; 120:1041-1049. [PMID: 27521635 DOI: 10.1016/j.funbio.2016.04.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Revised: 04/04/2016] [Accepted: 04/04/2016] [Indexed: 10/21/2022]
Abstract
Ochratoxin A (OTA) is a mycotoxin produced by some Aspergillus and Penicillium species that grow on economically important agricultural crops and food products. OTA is classified as Group 2B carcinogen and is potently nephrotoxic, which is the basis for its regulation in some jurisdictions. Using high resolution mass spectroscopy, OTA and ochratoxin B (OTB) were detected in liquid culture extracts of Penicillium thymicola DAOMC 180753 isolated from Canadian cheddar cheese. The genome of this strain was sequenced, assembled and annotated to probe for putative genes involved in OTA biosynthesis. Known OTA biosynthetic genes from Penicillium verrucosum or Penicillium nordicum, two related Penicillium species that produce OTA, were not found in P. thymicola. However, a gene cluster containing a polyketide synthase (PKS) and PKS-nonribosomal peptide synthase (NRPS) hybrid encoding genes were located in the P. thymicola genome that showed a high degree of similarity to OTA biosynthetic enzymes of Aspergillus carbonarius and Aspergillus ochraceus. This is the first report of ochratoxin from P. thymicola and a new record of the species in Canada.
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Affiliation(s)
- Hai D T Nguyen
- University of Ottawa, Department of Biology, 30 Marie-Curie Private, Ottawa, ON, K1N 6N5, Canada; Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada.
| | - David R McMullin
- Carleton University, Department of Chemistry, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Ekaterina Ponomareva
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada
| | - Robert Riley
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Kyle R Pomraning
- Pacific Northwest National Laboratory, Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, 3335 Innovation Boulevard, Richland, WA, 99354, USA
| | - Scott E Baker
- Pacific Northwest National Laboratory, Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, 3335 Innovation Boulevard, Richland, WA, 99354, USA
| | - Keith A Seifert
- University of Ottawa, Department of Biology, 30 Marie-Curie Private, Ottawa, ON, K1N 6N5, Canada; Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada
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Kerkhoven EJ, Pomraning KR, Baker SE, Nielsen J. Regulation of amino-acid metabolism controls flux to lipid accumulation in Yarrowia lipolytica. NPJ Syst Biol Appl 2016; 2:16005. [PMID: 28725468 PMCID: PMC5516929 DOI: 10.1038/npjsba.2016.5] [Citation(s) in RCA: 122] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 11/23/2015] [Accepted: 12/07/2015] [Indexed: 01/01/2023] Open
Abstract
Yarrowia lipolytica is a promising microbial cell factory for the production of lipids to be used as fuels and chemicals, but there are few studies on regulation of its metabolism. Here we performed the first integrated data analysis of Y. lipolytica grown in carbon and nitrogen limited chemostat cultures. We first reconstructed a genome-scale metabolic model and used this for integrative analysis of multilevel omics data. Metabolite profiling and lipidomics was used to quantify the cellular physiology, while regulatory changes were measured using RNAseq. Analysis of the data showed that lipid accumulation in Y. lipolytica does not involve transcriptional regulation of lipid metabolism but is associated with regulation of amino-acid biosynthesis, resulting in redirection of carbon flux during nitrogen limitation from amino acids to lipids. Lipid accumulation in Y. lipolytica at nitrogen limitation is similar to the overflow metabolism observed in many other microorganisms, e.g. ethanol production by Sacchromyces cerevisiae at nitrogen limitation.
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Affiliation(s)
- Eduard J Kerkhoven
- Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
| | - Kyle R Pomraning
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Scott E Baker
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jens Nielsen
- Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
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Schmoll M, Dattenböck C, Carreras-Villaseñor N, Mendoza-Mendoza A, Tisch D, Alemán MI, Baker SE, Brown C, Cervantes-Badillo MG, Cetz-Chel J, Cristobal-Mondragon GR, Delaye L, Esquivel-Naranjo EU, Frischmann A, Gallardo-Negrete JDJ, García-Esquivel M, Gomez-Rodriguez EY, Greenwood DR, Hernández-Oñate M, Kruszewska JS, Lawry R, Mora-Montes HM, Muñoz-Centeno T, Nieto-Jacobo MF, Nogueira Lopez G, Olmedo-Monfil V, Osorio-Concepcion M, Piłsyk S, Pomraning KR, Rodriguez-Iglesias A, Rosales-Saavedra MT, Sánchez-Arreguín JA, Seidl-Seiboth V, Stewart A, Uresti-Rivera EE, Wang CL, Wang TF, Zeilinger S, Casas-Flores S, Herrera-Estrella A. The Genomes of Three Uneven Siblings: Footprints of the Lifestyles of Three Trichoderma Species. Microbiol Mol Biol Rev 2016; 80:205-327. [PMID: 26864432 PMCID: PMC4771370 DOI: 10.1128/mmbr.00040-15] [Citation(s) in RCA: 125] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The genus Trichoderma contains fungi with high relevance for humans, with applications in enzyme production for plant cell wall degradation and use in biocontrol. Here, we provide a broad, comprehensive overview of the genomic content of these species for "hot topic" research aspects, including CAZymes, transport, transcription factors, and development, along with a detailed analysis and annotation of less-studied topics, such as signal transduction, genome integrity, chromatin, photobiology, or lipid, sulfur, and nitrogen metabolism in T. reesei, T. atroviride, and T. virens, and we open up new perspectives to those topics discussed previously. In total, we covered more than 2,000 of the predicted 9,000 to 11,000 genes of each Trichoderma species discussed, which is >20% of the respective gene content. Additionally, we considered available transcriptome data for the annotated genes. Highlights of our analyses include overall carbohydrate cleavage preferences due to the different genomic contents and regulation of the respective genes. We found light regulation of many sulfur metabolic genes. Additionally, a new Golgi 1,2-mannosidase likely involved in N-linked glycosylation was detected, as were indications for the ability of Trichoderma spp. to generate hybrid galactose-containing N-linked glycans. The genomic inventory of effector proteins revealed numerous compounds unique to Trichoderma, and these warrant further investigation. We found interesting expansions in the Trichoderma genus in several signaling pathways, such as G-protein-coupled receptors, RAS GTPases, and casein kinases. A particularly interesting feature absolutely unique to T. atroviride is the duplication of the alternative sulfur amino acid synthesis pathway.
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Affiliation(s)
- Monika Schmoll
- Austrian Institute of Technology, Department Health and Environment, Bioresources Unit, Tulln, Austria
| | - Christoph Dattenböck
- Austrian Institute of Technology, Department Health and Environment, Bioresources Unit, Tulln, Austria
| | | | | | - Doris Tisch
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Vienna, Austria
| | - Mario Ivan Alemán
- Cinvestav, Department of Genetic Engineering, Irapuato, Guanajuato, Mexico
| | - Scott E Baker
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Christopher Brown
- University of Otago, Department of Biochemistry and Genetics, Dunedin, New Zealand
| | | | - José Cetz-Chel
- LANGEBIO, National Laboratory of Genomics for Biodiversity, Cinvestav-Irapuato, Guanajuato, Mexico
| | | | - Luis Delaye
- Cinvestav, Department of Genetic Engineering, Irapuato, Guanajuato, Mexico
| | | | - Alexa Frischmann
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Vienna, Austria
| | | | - Monica García-Esquivel
- LANGEBIO, National Laboratory of Genomics for Biodiversity, Cinvestav-Irapuato, Guanajuato, Mexico
| | | | - David R Greenwood
- The University of Auckland, School of Biological Sciences, Auckland, New Zealand
| | - Miguel Hernández-Oñate
- LANGEBIO, National Laboratory of Genomics for Biodiversity, Cinvestav-Irapuato, Guanajuato, Mexico
| | - Joanna S Kruszewska
- Polish Academy of Sciences, Institute of Biochemistry and Biophysics, Laboratory of Fungal Glycobiology, Warsaw, Poland
| | - Robert Lawry
- Lincoln University, Bio-Protection Research Centre, Lincoln, Canterbury, New Zealand
| | | | | | | | | | | | | | - Sebastian Piłsyk
- Polish Academy of Sciences, Institute of Biochemistry and Biophysics, Laboratory of Fungal Glycobiology, Warsaw, Poland
| | - Kyle R Pomraning
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Aroa Rodriguez-Iglesias
- Austrian Institute of Technology, Department Health and Environment, Bioresources Unit, Tulln, Austria
| | | | | | - Verena Seidl-Seiboth
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Vienna, Austria
| | | | | | - Chih-Li Wang
- National Chung-Hsing University, Department of Plant Pathology, Taichung, Taiwan
| | - Ting-Fang Wang
- Academia Sinica, Institute of Molecular Biology, Taipei, Taiwan
| | - Susanne Zeilinger
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Vienna, Austria University of Innsbruck, Institute of Microbiology, Innsbruck, Austria
| | | | - Alfredo Herrera-Estrella
- LANGEBIO, National Laboratory of Genomics for Biodiversity, Cinvestav-Irapuato, Guanajuato, Mexico
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Pomraning KR, Kim YM, Nicora CD, Chu RK, Bredeweg EL, Purvine SO, Hu D, Metz TO, Baker SE. Multi-omics analysis reveals regulators of the response to nitrogen limitation in Yarrowia lipolytica. BMC Genomics 2016; 17:138. [PMID: 26911370 PMCID: PMC4766638 DOI: 10.1186/s12864-016-2471-2] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Accepted: 02/12/2016] [Indexed: 01/03/2023] Open
Abstract
Background Yarrowia lipolytica is an oleaginous ascomycete yeast that stores lipids in response to limitation of nitrogen. While the enzymatic pathways responsible for neutral lipid accumulation in Y. lipolytica are well characterized, regulation of these pathways has received little attention. We therefore sought to characterize the response to nitrogen limitation at system-wide levels, including the proteome, phosphoproteome and metabolome, to better understand how this organism regulates and controls lipid metabolism and to identify targets that may be manipulated to improve lipid yield. Results We found that ribosome structural genes are down-regulated under nitrogen limitation, during which nitrogen containing compounds (alanine, putrescine, spermidine and urea) are depleted and sugar alcohols and TCA cycle intermediates accumulate (citrate, fumarate and malate). We identified 1219 novel phosphorylation sites in Y. lipolytica, 133 of which change in their abundance during nitrogen limitation. Regulatory proteins, including kinases and DNA binding proteins, are particularly enriched for phosphorylation. Within lipid synthesis pathways, we found that ATP-citrate lyase, acetyl-CoA carboxylase and lecithin cholesterol acyl transferase are phosphorylated during nitrogen limitation while many of the proteins involved in β-oxidation are down-regulated, suggesting that storage lipid accumulation may be regulated by phosphorylation of key enzymes. Further, we identified short DNA elements that associate specific transcription factor families with up- and down-regulated genes. Conclusions Integration of metabolome, proteome and phosphoproteome data identifies lipid accumulation in response to nitrogen limitation as a two-fold result of increased production of acetyl-CoA from excess citrate and decreased capacity for β-oxidation. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2471-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kyle R Pomraning
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.
| | - Young-Mo Kim
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.
| | - Carrie D Nicora
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.
| | - Rosalie K Chu
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.
| | - Erin L Bredeweg
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.
| | - Samuel O Purvine
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.
| | - Dehong Hu
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.
| | - Thomas O Metz
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.
| | - Scott E Baker
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.
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Geng T, Bredeweg EL, Szymanski CJ, Liu B, Baker SE, Orr G, Evans JE, Kelly RT. Compartmentalized microchannel array for high-throughput analysis of single cell polarized growth and dynamics. Sci Rep 2015; 5:16111. [PMID: 26530004 PMCID: PMC4632079 DOI: 10.1038/srep16111] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 10/08/2015] [Indexed: 12/01/2022] Open
Abstract
Interrogating polarized growth is technologically challenging due to extensive cellular branching and uncontrollable environmental conditions in conventional assays. Here we present a robust and high-performance microfluidic system that enables observations of polarized growth with enhanced temporal and spatial control over prolonged periods. The system has built-in tunability and versatility to accommodate a variety of scientific applications requiring precisely controlled environments. Using the model filamentous fungus, Neurospora crassa, our microfluidic system enabled direct visualization and analysis of cellular heterogeneity in a clonal fungal cell population, nuclear distribution and dynamics at the subhyphal level, and quantitative dynamics of gene expression with single hyphal compartment resolution in response to carbon source starvation and exchange. Although the microfluidic device is demonstrated on filamentous fungi, the technology is immediately extensible to a wide array of other biosystems that exhibit similar polarized cell growth, with applications ranging from bioenergy production to human health.
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Affiliation(s)
- Tao Geng
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Erin L Bredeweg
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Craig J Szymanski
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Bingwen Liu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Scott E Baker
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Galya Orr
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - James E Evans
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Ryan T Kelly
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
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47
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Lichius A, Bidard F, Buchholz F, Le Crom S, Martin J, Schackwitz W, Austerlitz T, Grigoriev IV, Baker SE, Margeot A, Seiboth B, Kubicek CP. Erratum to: Genome sequencing of the Trichoderma reesei QM9136 mutant identifies a truncation of the transcriptional regulator XYR1 as the cause for its cellulase-negative phenotype. BMC Genomics 2015; 16:725. [PMID: 26395946 PMCID: PMC4580284 DOI: 10.1186/s12864-015-1917-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 09/10/2015] [Indexed: 11/10/2022] Open
Affiliation(s)
- Alexander Lichius
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, Vienna University of Technology, A-1060, Vienna, Austria
| | - Frédérique Bidard
- IFP Energies Nouvelles, 1-4 Avenue de Bois-Préau, 92852, Rueil-Malmaison, France
| | - Franziska Buchholz
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, Vienna University of Technology, A-1060, Vienna, Austria
| | - Stéphane Le Crom
- Sorbonne Universités, UPMC Université Paris 06, Institut de Biologie Paris Seine (IBPS), FR 3631, Département des Plateforme, F-75005, Paris, France
| | - Joel Martin
- US Department of Energy Joint Genome Institute, 2800 Mitchell Avenue, Walnut Creek, CA, 94598, USA
| | - Wendy Schackwitz
- US Department of Energy Joint Genome Institute, 2800 Mitchell Avenue, Walnut Creek, CA, 94598, USA
| | - Tina Austerlitz
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, Vienna University of Technology, A-1060, Vienna, Austria
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, 2800 Mitchell Avenue, Walnut Creek, CA, 94598, USA
| | - Scott E Baker
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Antoine Margeot
- IFP Energies Nouvelles, 1-4 Avenue de Bois-Préau, 92852, Rueil-Malmaison, France
| | - Bernhard Seiboth
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, Vienna University of Technology, A-1060, Vienna, Austria.
| | - Christian P Kubicek
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, Vienna University of Technology, A-1060, Vienna, Austria
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48
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Pomraning KR, Wei S, Karagiosis SA, Kim YM, Dohnalkova AC, Arey BW, Bredeweg EL, Orr G, Metz TO, Baker SE. Comprehensive Metabolomic, Lipidomic and Microscopic Profiling of Yarrowia lipolytica during Lipid Accumulation Identifies Targets for Increased Lipogenesis. PLoS One 2015; 10:e0123188. [PMID: 25905710 PMCID: PMC4408067 DOI: 10.1371/journal.pone.0123188] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 02/17/2015] [Indexed: 11/24/2022] Open
Abstract
Yarrowia lipolytica is an oleaginous ascomycete yeast that accumulates large amounts of lipids and has potential as a biofuel producing organism. Despite a growing scientific literature focused on lipid production by Y. lipolytica, there remain significant knowledge gaps regarding the key biological processes involved. We applied a combination of metabolomic and lipidomic profiling approaches as well as microscopic techniques to identify and characterize the key pathways involved in de novo lipid accumulation from glucose in batch cultured, wild-type Y. lipolytica. We found that lipids accumulated rapidly and peaked at 48 hours during the five day experiment, concurrent with a shift in amino acid metabolism. We also report that exhaustion of extracellular sugars coincided with thickening of the cell wall, suggesting that genes involved in cell wall biogenesis may be a useful target for improving the efficiency of lipid producing yeast strains.
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Affiliation(s)
- Kyle R. Pomraning
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States of America
| | - Siwei Wei
- Fundamental and Computer Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States of America
| | - Sue A. Karagiosis
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, United States of America
| | - Young-Mo Kim
- Fundamental and Computer Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States of America
| | - Alice C. Dohnalkova
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States of America
| | - Bruce W. Arey
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States of America
| | - Erin L. Bredeweg
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States of America
| | - Galya Orr
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States of America
| | - Thomas O. Metz
- Fundamental and Computer Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States of America
| | - Scott E. Baker
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States of America
- * E-mail:
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Baker SE, Shaw RF, Atkinson RPD, West P, Macdonald DW. Potential welfare impacts of kill-trapping European moles ( Talpa europaea) using scissor traps and Duffus traps: a post mortem examination study. Anim Welf 2015. [DOI: 10.7120/09627286.24.1.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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50
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Papillon-Smith J, Baker SE, Agbo C, Dahan MH. Pregnancy rates with intrauterine insemination: comparing 1999 and 2010 World Health Organization semen analysis norms. Reprod Biomed Online 2014; 30:392-400. [PMID: 25682304 DOI: 10.1016/j.rbmo.2014.12.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2014] [Revised: 12/07/2014] [Accepted: 12/09/2014] [Indexed: 10/24/2022]
Abstract
Over the past 30 years, The World Health Organization has serially measured norms for human sperm. In this study, 1999 and 2010 semen analysis norms as predictors of pregnancy were compared during intrauterine insemination (IUI). A retrospective cohort study was conducted using data collected from the Stanford Fertility Center, between 2005 and 2007, with 981 couples undergoing 2231 IUI cycles. Collected semen was categorized according to total motile sperm counts (TMSC): 'normal (N.) 1999 TMSC', 'abnormal (AbN.) 1999/N. 2010 TMSC', or 'AbN. 2010 TMSC'. Sample comparison was also based on individual semen parameters: 'N. 1999 WHO', 'AbN. 1999/N. 2010 WHO', or 'AbN. 2010 WHO'. Pregnancy (defined by beta-HCG concentration) rates were calculated. Data were compared using correlation coefficients, t-tests and chi-squared tests, with and without adjusting for confounders. Pregnancy rate comparison based on TMSC ('N. 1999 TMSC', 'AbN. 1999/N. 2010 TMSC' and 'AbN. 2010 TMSC') showed a negative correlation (r = -0.41, P = 0.05). Pregnancy rate did not differ when comparisons were based on the presence of abnormal parameters, even when controlling for confounders. Therefore, TMSC based on the 1999 parameters shows best correlation with pregnancy rate for IUI; updating these norms in 2010 has little clinical implication in infertile populations.
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Affiliation(s)
- J Papillon-Smith
- Department of Obstetrics and Gynecology, McGill University, 687 Pine Ave West, Montreal, QC, Canada H3A 1A1.
| | - S E Baker
- High School Student Summer Research Rotation, Stanford Medical School, 291 Campus Drive, Li Ka Shing Building, 3rd floor, Stanford, CA, USA
| | - C Agbo
- Stanford University School of Medicine, 291 Campus Drive, Li Ka Shing Building, 3rd floor, Stanford, CA, USA
| | - M H Dahan
- Department of Obstetrics and Gynecology, McGill University, 687 Pine Ave West, Montreal, QC, Canada H3A 1A1
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